chr7-82485924-C-T

Variant names:

• chr7-82485924-C-T
• rs10262537

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.582

Gnomad4 AMR AF: 0.285

Gnomad4 ASJ AF: 0.427

Gnomad4 EAS AF: 0.124

Gnomad4 SAS AF: 0.440

Gnomad4 FIN AF: 0.431

Gnomad4 NFE AF: 0.398

Gnomad4 OTH AF: 0.391

Alfa AF: 0.421 Hom.: 3638

Bravo AF: 0.422

Asia WGS AF: 0.270 AC: 943 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.66
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10262537; hg19: chr7-82115240;