rs10983837

Variant names:

• chr9-117936537-C-A
• rs10983837
• ENST00000665764.1:n.*17-35562C>A

Your query was ambiguous. Multiple possible variants found:

• chr9-117936537-C-A
• chr9-117936537-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000665764.1(ENSG00000285082):​n.*17-35562C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0253 in 151,904 control chromosomes in the GnomAD database, including 71 homozygotes. 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: 𝑓 0.025 (71 hom., cov: 31)
• Consequence: ENSG00000285082 ENST00000665764.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.116
• Publications: 1 publications found

Genes affected

ENSG00000285082 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0253 (3836/151904) while in subpopulation NFE AF = 0.0373 (2537/67966). AF 95% confidence interval is 0.0361. There are 71 homozygotes in GnomAd4. There are 1835 alleles in the male GnomAd4 subpopulation. Median coverage is 31. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 71 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285082	ENST00000665764.1	n.*17-35562C>A		intron_variant	Intron 2 of 6			ENSP00000499745.1
ENSG00000285082	ENST00000697636.1	n.*16+88382C>A		intron_variant	Intron 2 of 5			ENSP00000513366.1
ENSG00000284977	ENST00000697639.1	n.1053+88382C>A		intron_variant	Intron 7 of 12

Frequencies

GnomAD3 genomes AF: 0.0252 AC: 3832 AN: 151788 Hom.: 70 Cov.: 31

Gnomad AFR AF: 0.00649

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.0257

Gnomad ASJ AF: 0.0363

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.0201

Gnomad FIN AF: 0.0299

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0373

Gnomad OTH AF: 0.0322

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

GnomAD4 genome AF: 0.0253 AC: 3836 AN: 151904 Hom.: 71 Cov.: 31 AF XY: 0.0247 AC XY: 1835 AN XY: 74244

African (AFR) AF: 0.00647 AC: 268 AN: 41422

American (AMR) AF: 0.0257 AC: 391 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.0363 AC: 126 AN: 3468

East Asian (EAS) AF: 0.000387 AC: 2 AN: 5172

South Asian (SAS) AF: 0.0208 AC: 100 AN: 4812

European-Finnish (FIN) AF: 0.0299 AC: 315 AN: 10522

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0373 AC: 2537 AN: 67966

Other (OTH) AF: 0.0319 AC: 67 AN: 2100

Alfa AF: 0.0339 Hom.: 156

Bravo AF: 0.0245

Asia WGS AF: 0.0130 AC: 46 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.1
DANN	Benign	0.38
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs10983837; hg19: chr9-120698815;