17-19337659-G-T

Variant names:

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

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001321218.2(B9D1):​c.*61C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 34)
  • Exomes 𝑓: 0.000024 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: B9D1 NM_001321218.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.01

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]

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
B9D1	NM_001321218.2	c.*61C>A		3_prime_UTR_variant	Exon 7 of 7		NP_001308147.1
B9D1	NM_001321219.2	c.*26C>A		3_prime_UTR_variant	Exon 6 of 6		NP_001308148.1
B9D1	NM_001368769.2	c.*61C>A		3_prime_UTR_variant	Exon 7 of 7		NP_001355698.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
B9D1	ENST00000671102	c.*61C>A		3_prime_UTR_variant	Exon 8 of 8			ENSP00000499690.1
B9D1	ENST00000675510	c.*26C>A		3_prime_UTR_variant	Exon 6 of 6			ENSP00000501817.1
B9D1	ENST00000674596	c.*26C>A		3_prime_UTR_variant	Exon 8 of 8			ENSP00000501877.1
B9D1	ENST00000582857.2	c.*61C>A		3_prime_UTR_variant	Exon 7 of 7	4		ENSP00000463165.2

Frequencies

GnomAD3 genomes Cov.: 34

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000237 AC: 32 AN: 1349966 Hom.: 0 Cov.: 23 AF XY: 0.0000211 AC XY: 14 AN XY: 664380

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000305

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 34

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.22
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11652712; hg19: chr17-19240972;