chr11-17477320-C-T

Variant names:

• chr11-17477320-C-T
• rs184908312
• ENST00000662030.2:n.200+589C>T

Variant summary

Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP4_Strong BP6 BS1

The ENST00000662030.2(ENSG00000287898):​n.200+589C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00076 in 128,900 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

• Frequency: Genomes: 𝑓 0.00076 (1 hom., cov: 32)
• Consequence: ENSG00000287898 ENST00000662030.2 intron
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:2 B:1
• Conservation: PhyloP100: -0.906
• Publications: 1 publications found

Genes affected

ENSG00000287898 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BP6: Variant 11-17477320-C-T is Benign according to our data. Variant chr11-17477320-C-T is described in ClinVar as Conflicting_classifications_of_pathogenicity. ClinVar VariationId is 434041.
• BS1: Variant frequency is greater than expected in population eas. GnomAd4 allele frequency = 0.00076 (98/128900) while in subpopulation EAS AF = 0.0203 (89/4386). AF 95% confidence interval is 0.0169. There are 1 homozygotes in GnomAd4. There are 63 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000662030.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287898	ENST00000662030.2		n.200+589C>T		intron	N/A
	ENSG00000287898	ENST00000666786.2		n.153+266C>T		intron	N/A
	ENSG00000287898	ENST00000719322.1		n.150+1034C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.000761 AC: 98 AN: 128786 Hom.: 1 Cov.: 32

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000169

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.0203

Gnomad SAS AF: 0.000800

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000533

Gnomad OTH AF: 0.000562

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.000760 AC: 98 AN: 128900 Hom.: 1 Cov.: 32 AF XY: 0.00100 AC XY: 63 AN XY: 62854

African (AFR) AF: 0.00 AC: 0 AN: 37962

American (AMR) AF: 0.000169 AC: 2 AN: 11830

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3110

East Asian (EAS) AF: 0.0203 AC: 89 AN: 4386

South Asian (SAS) AF: 0.000800 AC: 3 AN: 3748

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 8772

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 262

European-Non Finnish (NFE) AF: 0.0000533 AC: 3 AN: 56242

Other (OTH) AF: 0.000555 AC: 1 AN: 1802

Alfa AF: 0.000142 Hom.: 0

Bravo AF: 0.000922

Asia WGS AF: 0.00549 AC: 19 AN: 3478

ClinVar

ClinVar submissions as Germline

Significance: Conflicting classifications of pathogenicity

Revision: criteria provided, conflicting classifications

Pathogenic	VUS	Benign	Condition
-	1	-	Maturity onset diabetes mellitus in young (1)
-	-	1	not specified (1)
-	1	-	Transitory neonatal diabetes mellitus (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.79
DANN	Benign	0.73
PhyloP100		-0.91
PromoterAI		-0.018	Neutral

Splicing

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

Other links and lift over

dbSNP: rs184908312; hg19: chr11-17498867;