ENST00000671102:c.*61C>T

Variant names:

• chr17-19337659-G-A
• rs11652712
• ENST00000671102.1:c.*61C>T

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The ENST00000671102.1(B9D1):​c.*61C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.969 in 1,502,002 control chromosomes in the GnomAD database, including 708,316 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.97 (71418 hom., cov: 34)
  • Exomes 𝑓: 0.97 (636898 hom.)
• Consequence: B9D1 ENST00000671102.1 3_prime_UTR
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:4
• Conservation: PhyloP100: -2.01
• Publications: 10 publications found

Genes affected

B9D1 (HGNC:24123): (B9 domain containing 1) This gene encodes a B9 domain-containing protein, one of several that are involved in ciliogenesis. Alterations in expression of this gene have been found in a family with Meckel syndrome. Meckel syndrome has been associated with at least six different genes. This gene is located within the Smith-Magenis syndrome region on chromosome 17. [provided by RefSeq, Mar 2016]

B9D1 Gene-Disease associations (from GenCC):

• ciliopathy

  Inheritance: AR Classification: DEFINITIVE Submitted by: ClinGen
• Joubert syndrome 27

  Inheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
• Meckel syndrome, type 9

  Inheritance: AR Classification: STRONG, MODERATE Submitted by: G2P, Genomics England PanelApp
• Joubert syndrome

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
• Meckel syndrome

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Benign. The variant received -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BP6: Variant 17-19337659-G-A is Benign according to our data. Variant chr17-19337659-G-A is described in ClinVar as Benign. ClinVar VariationId is 1192493.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.983 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000671102.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	B9D1	NM_001321218.2		c.*61C>T		3_prime_UTR	Exon 7 of 7	NP_001308147.1
	B9D1	NM_001321219.2		c.*26C>T		3_prime_UTR	Exon 6 of 6	NP_001308148.1	A0A6Q8PFJ7
	B9D1	NM_001368769.2		c.*61C>T		3_prime_UTR	Exon 7 of 7	NP_001355698.1	J3QKN6

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	B9D1	ENST00000671102.1		c.*61C>T		3_prime_UTR	Exon 8 of 8	ENSP00000499690.1	A0A590UK40
	B9D1	ENST00000675510.1		c.*26C>T		3_prime_UTR	Exon 6 of 6	ENSP00000501817.1	A0A6Q8PFJ7
	B9D1	ENST00000674596.1		c.*26C>T		3_prime_UTR	Exon 8 of 8	ENSP00000501877.1	A0A6Q8PFN7

Frequencies

GnomAD3 genomes AF: 0.967 AC: 147131 AN: 152214 Hom.: 71371 Cov.: 34

Gnomad AFR AF: 0.991

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.873

Gnomad ASJ AF: 0.989

Gnomad EAS AF: 0.852

Gnomad SAS AF: 0.803

Gnomad FIN AF: 0.983

Gnomad MID AF: 0.981

Gnomad NFE AF: 0.989

Gnomad OTH AF: 0.969

GnomAD2 exomes AF: 0.905 AC: 121376 AN: 134102 AF XY: 0.906

Gnomad AFR exome AF: 0.991

Gnomad AMR exome AF: 0.772

Gnomad ASJ exome AF: 0.987

Gnomad EAS exome AF: 0.835

Gnomad FIN exome AF: 0.986

Gnomad NFE exome AF: 0.989

Gnomad OTH exome AF: 0.945

GnomAD4 exome AF: 0.970 AC: 1308766 AN: 1349670 Hom.: 636898 Cov.: 23 AF XY: 0.965 AC XY: 641159 AN XY: 664218

African (AFR) AF: 0.993 AC: 30680 AN: 30910

American (AMR) AF: 0.787 AC: 27911 AN: 35472

Ashkenazi Jewish (ASJ) AF: 0.986 AC: 24566 AN: 24918

East Asian (EAS) AF: 0.863 AC: 30395 AN: 35202

South Asian (SAS) AF: 0.810 AC: 63634 AN: 78560

European-Finnish (FIN) AF: 0.985 AC: 33173 AN: 33676

Middle Eastern (MID) AF: 0.972 AC: 5407 AN: 5562

European-Non Finnish (NFE) AF: 0.990 AC: 1038480 AN: 1048730

Other (OTH) AF: 0.963 AC: 54520 AN: 56640

GnomAD4 genome AF: 0.967 AC: 147235 AN: 152332 Hom.: 71418 Cov.: 34 AF XY: 0.960 AC XY: 71539 AN XY: 74488

African (AFR) AF: 0.991 AC: 41210 AN: 41584

American (AMR) AF: 0.873 AC: 13355 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.989 AC: 3435 AN: 3472

East Asian (EAS) AF: 0.851 AC: 4396 AN: 5164

South Asian (SAS) AF: 0.805 AC: 3886 AN: 4830

European-Finnish (FIN) AF: 0.983 AC: 10448 AN: 10626

Middle Eastern (MID) AF: 0.980 AC: 288 AN: 294

European-Non Finnish (NFE) AF: 0.989 AC: 67258 AN: 68040

Other (OTH) AF: 0.969 AC: 2047 AN: 2112

Alfa AF: 0.976 Hom.: 86111

Bravo AF: 0.962

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	2	not provided (2)
-	-	1	Joubert syndrome 27 (1)
-	-	1	Meckel syndrome, type 9 (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.59
DANN	Benign	0.40
PhyloP100		-2.0
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs11652712; hg19: chr17-19240972;