rs10513311

Variant names:

• chr9-117846442-C-A
• rs10513311
• ENST00000697666.1:c.141-1623C>A

Your query was ambiguous. Multiple possible variants found:

• chr9-117846442-C-A
• chr9-117846442-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000697666.1(ENSG00000285082):​c.141-1623C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.436 in 151,880 control chromosomes in the GnomAD database, including 15,027 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 0.44 (15027 hom., cov: 32)
• Consequence: ENSG00000285082 ENST00000697666.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.353
• Publications: 4 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).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.504 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000697666.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285082	ENST00000697666.1		c.141-1623C>A		intron	N/A	ENSP00000513391.1	A0A8V8TMK6
	ENSG00000285082	ENST00000646089.2		c.94-1623C>A		intron	N/A	ENSP00000496197.1	A0A2R8YGN2
	ENSG00000285082	ENST00000697637.1		c.94-1623C>A		intron	N/A	ENSP00000513367.1	A0A2R8YGN2

Frequencies

GnomAD3 genomes AF: 0.436 AC: 66142 AN: 151762 Hom.: 15033 Cov.: 32

Gnomad AFR AF: 0.367

Gnomad AMI AF: 0.567

Gnomad AMR AF: 0.374

Gnomad ASJ AF: 0.538

Gnomad EAS AF: 0.204

Gnomad SAS AF: 0.301

Gnomad FIN AF: 0.448

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.508

Gnomad OTH AF: 0.463

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

GnomAD4 genome AF: 0.436 AC: 66154 AN: 151880 Hom.: 15027 Cov.: 32 AF XY: 0.429 AC XY: 31876 AN XY: 74252

African (AFR) AF: 0.367 AC: 15206 AN: 41396

American (AMR) AF: 0.374 AC: 5701 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.538 AC: 1865 AN: 3466

East Asian (EAS) AF: 0.203 AC: 1049 AN: 5156

South Asian (SAS) AF: 0.300 AC: 1444 AN: 4814

European-Finnish (FIN) AF: 0.448 AC: 4729 AN: 10562

Middle Eastern (MID) AF: 0.510 AC: 149 AN: 292

European-Non Finnish (NFE) AF: 0.508 AC: 34521 AN: 67912

Other (OTH) AF: 0.461 AC: 974 AN: 2112

Alfa AF: 0.474 Hom.: 36732

Bravo AF: 0.426

Asia WGS AF: 0.270 AC: 941 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.32
DANN	Benign	0.70
PhyloP100		-0.35

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10513311;

hg19: chr9-120608720;