chr6-37622021-G-T

Variant names:

• chr6-37622021-G-T
• rs7751500

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 0.849 in 152,118 control chromosomes in the GnomAD database, including 55,002 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 0.85 (55002 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0750
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 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: 0.849 AC: 129020 AN: 152000 Hom.: 54976 Cov.: 31

Gnomad AFR AF: 0.774

Gnomad AMI AF: 0.906

Gnomad AMR AF: 0.890

Gnomad ASJ AF: 0.861

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.890

Gnomad FIN AF: 0.914

Gnomad MID AF: 0.848

Gnomad NFE AF: 0.859

Gnomad OTH AF: 0.840

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

GnomAD4 genome AF: 0.849 AC: 129097 AN: 152118 Hom.: 55002 Cov.: 31 AF XY: 0.852 AC XY: 63319 AN XY: 74356

African (AFR) AF: 0.774 AC: 32092 AN: 41456

American (AMR) AF: 0.890 AC: 13620 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.861 AC: 2990 AN: 3472

East Asian (EAS) AF: 0.998 AC: 5170 AN: 5182

South Asian (SAS) AF: 0.888 AC: 4264 AN: 4800

European-Finnish (FIN) AF: 0.914 AC: 9675 AN: 10588

Middle Eastern (MID) AF: 0.837 AC: 246 AN: 294

European-Non Finnish (NFE) AF: 0.859 AC: 58434 AN: 67996

Other (OTH) AF: 0.841 AC: 1780 AN: 2116

Alfa AF: 0.836 Hom.: 24328

Bravo AF: 0.845

Asia WGS AF: 0.928 AC: 3228 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.0
DANN	Benign	0.58
PhyloP100		0.075

Splicing

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

Other links and lift over

dbSNP: rs7751500; hg19: chr6-37589797;