rs10269143

Variant names:

• chr7-17359359-T-A
• rs10269143
• ENST00000637807.1:c.2373+19131T>A

Your query was ambiguous. Multiple possible variants found:

• chr7-17359359-T-A
• chr7-17359359-T-G

Variant summary

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

The ENST00000637807.1(ENSG00000283321):​c.2373+19131T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.272 in 151,968 control chromosomes in the GnomAD database, including 7,101 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 0.27 (7101 hom., cov: 32)
• Consequence: ENSG00000283321 ENST00000637807.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0150
• Publications: 3 publications found

Genes affected

ENSG00000283321 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.488 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000637807.1. 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
	ENSG00000283321	ENST00000637807.1	TSL:5	c.2373+19131T>A		intron	N/A	ENSP00000490530.1

Frequencies

GnomAD3 genomes AF: 0.272 AC: 41264 AN: 151846 Hom.: 7068 Cov.: 32

Gnomad AFR AF: 0.493

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.167

Gnomad EAS AF: 0.385

Gnomad SAS AF: 0.199

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.268

Gnomad NFE AF: 0.176

Gnomad OTH AF: 0.249

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

GnomAD4 genome AF: 0.272 AC: 41341 AN: 151968 Hom.: 7101 Cov.: 32 AF XY: 0.270 AC XY: 20065 AN XY: 74280

African (AFR) AF: 0.493 AC: 20437 AN: 41418

American (AMR) AF: 0.200 AC: 3058 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.167 AC: 579 AN: 3472

East Asian (EAS) AF: 0.386 AC: 1992 AN: 5162

South Asian (SAS) AF: 0.197 AC: 949 AN: 4812

European-Finnish (FIN) AF: 0.155 AC: 1636 AN: 10548

Middle Eastern (MID) AF: 0.277 AC: 81 AN: 292

European-Non Finnish (NFE) AF: 0.176 AC: 11989 AN: 67964

Other (OTH) AF: 0.246 AC: 519 AN: 2110

Alfa AF: 0.228 Hom.: 654

Bravo AF: 0.288

Asia WGS AF: 0.255 AC: 887 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.19
DANN	Benign	0.25
PhyloP100		-0.015

Splicing

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

Other links and lift over

dbSNP: rs10269143; hg19: chr7-17398983;