6-7645798-A-G

Variant names:

• chr6-7645798-A-G
• rs6938572

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 0.64 in 152,000 control chromosomes in the GnomAD database, including 31,561 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 (31561 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.629
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.712 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: 0.640 AC: 97157 AN: 151882 Hom.: 31524 Cov.: 31

Gnomad AFR AF: 0.530

Gnomad AMI AF: 0.753

Gnomad AMR AF: 0.723

Gnomad ASJ AF: 0.730

Gnomad EAS AF: 0.688

Gnomad SAS AF: 0.601

Gnomad FIN AF: 0.663

Gnomad MID AF: 0.811

Gnomad NFE AF: 0.674

Gnomad OTH AF: 0.700

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

GnomAD4 genome AF: 0.640 AC: 97249 AN: 152000 Hom.: 31561 Cov.: 31 AF XY: 0.640 AC XY: 47496 AN XY: 74254

African (AFR) AF: 0.531 AC: 21984 AN: 41434

American (AMR) AF: 0.723 AC: 11045 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.730 AC: 2533 AN: 3470

East Asian (EAS) AF: 0.688 AC: 3541 AN: 5148

South Asian (SAS) AF: 0.603 AC: 2899 AN: 4810

European-Finnish (FIN) AF: 0.663 AC: 7014 AN: 10580

Middle Eastern (MID) AF: 0.817 AC: 237 AN: 290

European-Non Finnish (NFE) AF: 0.674 AC: 45831 AN: 67962

Other (OTH) AF: 0.699 AC: 1480 AN: 2116

Alfa AF: 0.651 Hom.: 13010

Bravo AF: 0.643

Asia WGS AF: 0.669 AC: 2329 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.79
DANN	Benign	0.42
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs6938572; hg19: chr6-7646031;