rs9631436

Variant names:

• chr3-105871276-G-A
• rs9631436
• ENST00000766643.1:n.235+1924G>A

Variant summary

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

The ENST00000766643.1(ENSG00000288848):​n.235+1924G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.213 in 152,078 control chromosomes in the GnomAD database, including 3,655 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 0.21 (3655 hom., cov: 32)
• Consequence: ENSG00000288848 ENST00000766643.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.164
• Publications: 1 publications found

Genes affected

ENSG00000288848 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.406 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000766643.1. 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
	ENSG00000288848	ENST00000766643.1		n.235+1924G>A		intron	N/A
	ENSG00000288848	ENST00000766644.1		n.201+211G>A		intron	N/A
	ENSG00000288848	ENST00000766645.1		n.138+1956G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.213 AC: 32430 AN: 151960 Hom.: 3646 Cov.: 32

Gnomad AFR AF: 0.226

Gnomad AMI AF: 0.246

Gnomad AMR AF: 0.229

Gnomad ASJ AF: 0.154

Gnomad EAS AF: 0.421

Gnomad SAS AF: 0.232

Gnomad FIN AF: 0.176

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.194

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.213 AC: 32460 AN: 152078 Hom.: 3655 Cov.: 32 AF XY: 0.215 AC XY: 15989 AN XY: 74348

African (AFR) AF: 0.226 AC: 9370 AN: 41480

American (AMR) AF: 0.229 AC: 3494 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.154 AC: 535 AN: 3470

East Asian (EAS) AF: 0.421 AC: 2178 AN: 5176

South Asian (SAS) AF: 0.232 AC: 1121 AN: 4822

European-Finnish (FIN) AF: 0.176 AC: 1862 AN: 10554

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.194 AC: 13215 AN: 67986

Other (OTH) AF: 0.201 AC: 423 AN: 2106

Alfa AF: 0.205 Hom.: 439

Bravo AF: 0.221

Asia WGS AF: 0.316 AC: 1100 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.4
DANN	Benign	0.52
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs9631436; hg19: chr3-105590120;