rs7913244

Variant names:

• chr10-10142402-T-A
• rs7913244
• ENST00000738164.1:n.299+51630T>A

Your query was ambiguous. Multiple possible variants found:

• chr10-10142402-T-A
• chr10-10142402-T-C
• chr10-10142402-T-G

Variant summary

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

The ENST00000738164.1(ENSG00000296323):​n.299+51630T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.194 in 152,130 control chromosomes in the GnomAD database, including 3,520 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 0.19 (3520 hom., cov: 32)
• Consequence: ENSG00000296323 ENST00000738164.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.292
• Publications: 1 publications found

Genes affected

ENSG00000296323 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.367 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000738164.1. 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
	ENSG00000296323	ENST00000738164.1		n.299+51630T>A		intron	N/A
	ENSG00000296323	ENST00000738165.1		n.326+51630T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.194 AC: 29498 AN: 152014 Hom.: 3505 Cov.: 32

Gnomad AFR AF: 0.286

Gnomad AMI AF: 0.206

Gnomad AMR AF: 0.248

Gnomad ASJ AF: 0.166

Gnomad EAS AF: 0.381

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.0676

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.131

Gnomad OTH AF: 0.197

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

GnomAD4 genome AF: 0.194 AC: 29560 AN: 152130 Hom.: 3520 Cov.: 32 AF XY: 0.197 AC XY: 14620 AN XY: 74366

African (AFR) AF: 0.287 AC: 11893 AN: 41480

American (AMR) AF: 0.247 AC: 3779 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.166 AC: 577 AN: 3472

East Asian (EAS) AF: 0.381 AC: 1968 AN: 5164

South Asian (SAS) AF: 0.208 AC: 1005 AN: 4826

European-Finnish (FIN) AF: 0.0676 AC: 716 AN: 10598

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.132 AC: 8943 AN: 67994

Other (OTH) AF: 0.199 AC: 420 AN: 2110

Alfa AF: 0.146 Hom.: 267

Bravo AF: 0.212

Asia WGS AF: 0.317 AC: 1101 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.3
DANN	Benign	0.65
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs7913244; hg19: chr10-10184365;