6-70615020-G-T

Variant names:

• chr6-70615020-G-T
• rs1524738

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 0.598 in 151,924 control chromosomes in the GnomAD database, including 27,461 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 0.60 (27461 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.100
• Publications: 5 publications found

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 (AMR) allele frequency at 95% confidence interval = 0.677 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.597 AC: 90703 AN: 151806 Hom.: 27409 Cov.: 32

Gnomad AFR AF: 0.654

Gnomad AMI AF: 0.545

Gnomad AMR AF: 0.688

Gnomad ASJ AF: 0.528

Gnomad EAS AF: 0.527

Gnomad SAS AF: 0.529

Gnomad FIN AF: 0.576

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.561

Gnomad OTH AF: 0.595

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

GnomAD4 genome AF: 0.598 AC: 90809 AN: 151924 Hom.: 27461 Cov.: 32 AF XY: 0.599 AC XY: 44435 AN XY: 74234

African (AFR) AF: 0.654 AC: 27094 AN: 41440

American (AMR) AF: 0.688 AC: 10501 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.528 AC: 1832 AN: 3470

East Asian (EAS) AF: 0.527 AC: 2717 AN: 5152

South Asian (SAS) AF: 0.528 AC: 2543 AN: 4812

European-Finnish (FIN) AF: 0.576 AC: 6052 AN: 10512

Middle Eastern (MID) AF: 0.527 AC: 155 AN: 294

European-Non Finnish (NFE) AF: 0.561 AC: 38154 AN: 67960

Other (OTH) AF: 0.599 AC: 1266 AN: 2112

Alfa AF: 0.577 Hom.: 32020

Bravo AF: 0.610

Asia WGS AF: 0.586 AC: 2039 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	5.3
DANN	Benign	0.77
PhyloP100		0.10

Splicing

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

Other links and lift over

dbSNP: rs1524738; hg19: chr6-71324723; COSMIC: COSV69404425;