rs682238

Variant names:

• chr6-62450242-C-G
• rs682238

Your query was ambiguous. Multiple possible variants found:

• chr6-62450242-C-G
• chr6-62450242-C-T

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 0.875 in 152,150 control chromosomes in the GnomAD database, including 58,425 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 0.88 (58425 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00700
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.923 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: 0.876 AC: 133115 AN: 152032 Hom.: 58386 Cov.: 32

Gnomad AFR AF: 0.931

Gnomad AMI AF: 0.818

Gnomad AMR AF: 0.876

Gnomad ASJ AF: 0.848

Gnomad EAS AF: 0.859

Gnomad SAS AF: 0.779

Gnomad FIN AF: 0.884

Gnomad MID AF: 0.791

Gnomad NFE AF: 0.852

Gnomad OTH AF: 0.854

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

GnomAD4 genome AF: 0.875 AC: 133204 AN: 152150 Hom.: 58425 Cov.: 32 AF XY: 0.876 AC XY: 65155 AN XY: 74374

African (AFR) AF: 0.931 AC: 38684 AN: 41542

American (AMR) AF: 0.876 AC: 13378 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.848 AC: 2943 AN: 3472

East Asian (EAS) AF: 0.858 AC: 4449 AN: 5184

South Asian (SAS) AF: 0.779 AC: 3756 AN: 4824

European-Finnish (FIN) AF: 0.884 AC: 9343 AN: 10564

Middle Eastern (MID) AF: 0.779 AC: 229 AN: 294

European-Non Finnish (NFE) AF: 0.852 AC: 57884 AN: 67978

Other (OTH) AF: 0.849 AC: 1792 AN: 2110

Alfa AF: 0.862 Hom.: 6599

Bravo AF: 0.878

Asia WGS AF: 0.781 AC: 2693 AN: 3446

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.7
DANN	Benign	0.66
PhyloP100		-0.0070

Splicing

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

Other links and lift over

dbSNP: rs682238; hg19: chr6-63160147;