6-37206969-A-G

Variant names:

• chr6-37206969-A-G
• rs1680005

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 0.643 in 152,042 control chromosomes in the GnomAD database, including 31,533 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 0.64 (31533 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.08
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.828 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: 0.643 AC: 97743 AN: 151924 Hom.: 31522 Cov.: 32

Gnomad AFR AF: 0.611

Gnomad AMI AF: 0.673

Gnomad AMR AF: 0.660

Gnomad ASJ AF: 0.612

Gnomad EAS AF: 0.850

Gnomad SAS AF: 0.711

Gnomad FIN AF: 0.591

Gnomad MID AF: 0.772

Gnomad NFE AF: 0.647

Gnomad OTH AF: 0.646

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

GnomAD4 genome AF: 0.643 AC: 97792 AN: 152042 Hom.: 31533 Cov.: 32 AF XY: 0.644 AC XY: 47880 AN XY: 74318

African (AFR) AF: 0.611 AC: 25309 AN: 41454

American (AMR) AF: 0.661 AC: 10094 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.612 AC: 2124 AN: 3472

East Asian (EAS) AF: 0.849 AC: 4394 AN: 5174

South Asian (SAS) AF: 0.711 AC: 3426 AN: 4820

European-Finnish (FIN) AF: 0.591 AC: 6245 AN: 10562

Middle Eastern (MID) AF: 0.759 AC: 223 AN: 294

European-Non Finnish (NFE) AF: 0.647 AC: 44001 AN: 67970

Other (OTH) AF: 0.646 AC: 1364 AN: 2110

Alfa AF: 0.647 Hom.: 95675

Bravo AF: 0.645

Asia WGS AF: 0.730 AC: 2532 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.4
DANN	Benign	0.33
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs1680005; hg19: chr6-37174745;