chr7-62616585-G-T

Variant names:

• chr7-62616585-G-T
• rs2382591

Variant summary

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

The variant allele was found at a frequency of 0.15 in 151,948 control chromosomes in the GnomAD database, including 1,980 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 0.15 (1980 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.296 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: 0.150 AC: 22789 AN: 151830 Hom.: 1975 Cov.: 32

Gnomad AFR AF: 0.0883

Gnomad AMI AF: 0.130

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.133

Gnomad EAS AF: 0.307

Gnomad SAS AF: 0.213

Gnomad FIN AF: 0.230

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.152

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

GnomAD4 genome AF: 0.150 AC: 22804 AN: 151948 Hom.: 1980 Cov.: 32 AF XY: 0.157 AC XY: 11678 AN XY: 74242

African (AFR) AF: 0.0882 AC: 3659 AN: 41502

American (AMR) AF: 0.182 AC: 2768 AN: 15178

Ashkenazi Jewish (ASJ) AF: 0.133 AC: 462 AN: 3466

East Asian (EAS) AF: 0.309 AC: 1584 AN: 5134

South Asian (SAS) AF: 0.214 AC: 1030 AN: 4820

European-Finnish (FIN) AF: 0.230 AC: 2434 AN: 10566

Middle Eastern (MID) AF: 0.123 AC: 36 AN: 292

European-Non Finnish (NFE) AF: 0.153 AC: 10388 AN: 67972

Other (OTH) AF: 0.154 AC: 324 AN: 2106

Alfa AF: 0.0798 Hom.: 103

Bravo AF: 0.141

Asia WGS AF: 0.256 AC: 891 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.3
DANN	Benign	0.51

Splicing

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

Other links and lift over

dbSNP: rs2382591; hg19: chr7-62076963;