rs10936632

Variant names:

• chr3-170412314-C-A
• rs10936632
• ENST00000468232.1:n.263-483C>A

Your query was ambiguous. Multiple possible variants found:

• chr3-170412314-C-A
• chr3-170412314-C-G

Variant summary

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

The ENST00000468232.1(ENSG00000242578):​n.263-483C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.411 in 150,074 control chromosomes in the GnomAD database, including 13,991 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 0.41 (13991 hom., cov: 26)
• Consequence: ENSG00000242578 ENST00000468232.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.205
• Publications: 57 publications found

Genes affected

ENSG00000242578 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.523 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000468232.1. 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
	ENSG00000242578	ENST00000468232.1	TSL:3	n.263-483C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.412 AC: 61744 AN: 149960 Hom.: 13989 Cov.: 26

Gnomad AFR AF: 0.233

Gnomad AMI AF: 0.424

Gnomad AMR AF: 0.352

Gnomad ASJ AF: 0.403

Gnomad EAS AF: 0.295

Gnomad SAS AF: 0.540

Gnomad FIN AF: 0.544

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.514

Gnomad OTH AF: 0.387

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

GnomAD4 genome AF: 0.411 AC: 61746 AN: 150074 Hom.: 13991 Cov.: 26 AF XY: 0.411 AC XY: 30086 AN XY: 73168

African (AFR) AF: 0.232 AC: 9458 AN: 40698

American (AMR) AF: 0.352 AC: 5278 AN: 15014

Ashkenazi Jewish (ASJ) AF: 0.403 AC: 1395 AN: 3460

East Asian (EAS) AF: 0.294 AC: 1491 AN: 5066

South Asian (SAS) AF: 0.541 AC: 2553 AN: 4720

European-Finnish (FIN) AF: 0.544 AC: 5566 AN: 10228

Middle Eastern (MID) AF: 0.279 AC: 81 AN: 290

European-Non Finnish (NFE) AF: 0.514 AC: 34739 AN: 67612

Other (OTH) AF: 0.385 AC: 802 AN: 2082

Alfa AF: 0.488 Hom.: 4531

Bravo AF: 0.385

Asia WGS AF: 0.420 AC: 1463 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.9
DANN	Benign	0.78
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs10936632; hg19: chr3-170130102;