rs10262537

Variant names:

• chr7-82485924-C-T
• rs10262537
• ENST00000772831.1:n.172+14133C>T

Variant summary

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

The ENST00000772831.1(ENSG00000300590):​n.172+14133C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.432 in 151,680 control chromosomes in the GnomAD database, including 15,094 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 0.43 (15094 hom., cov: 32)
• Consequence: ENSG00000300590 ENST00000772831.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15
• Publications: 3 publications found

Genes affected

ENSG00000300590 (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 (AFR) allele frequency at 95% confidence interval = 0.576 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000772831.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000300590	ENST00000772831.1		n.172+14133C>T		intron	N/A
	ENSG00000300590	ENST00000772832.1		n.164-8076C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.432 AC: 65446 AN: 151562 Hom.: 15075 Cov.: 32

Gnomad AFR AF: 0.582

Gnomad AMI AF: 0.381

Gnomad AMR AF: 0.285

Gnomad ASJ AF: 0.427

Gnomad EAS AF: 0.124

Gnomad SAS AF: 0.441

Gnomad FIN AF: 0.431

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.398

Gnomad OTH AF: 0.395

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

GnomAD4 genome AF: 0.432 AC: 65505 AN: 151680 Hom.: 15094 Cov.: 32 AF XY: 0.430 AC XY: 31892 AN XY: 74082

African (AFR) AF: 0.582 AC: 24073 AN: 41330

American (AMR) AF: 0.285 AC: 4351 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.427 AC: 1478 AN: 3460

East Asian (EAS) AF: 0.124 AC: 641 AN: 5158

South Asian (SAS) AF: 0.440 AC: 2120 AN: 4816

European-Finnish (FIN) AF: 0.431 AC: 4504 AN: 10462

Middle Eastern (MID) AF: 0.425 AC: 124 AN: 292

European-Non Finnish (NFE) AF: 0.398 AC: 27042 AN: 67884

Other (OTH) AF: 0.391 AC: 825 AN: 2108

Alfa AF: 0.406 Hom.: 5700

Bravo AF: 0.422

Asia WGS AF: 0.270 AC: 943 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	0.66
DANN	Benign	0.48
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs10262537; hg19: chr7-82115240;