6-45809610-A-G

Variant names:

• chr6-45809610-A-G
• rs7746680

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 0.6 in 151,762 control chromosomes in the GnomAD database, including 30,958 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 (30958 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.288
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.758 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: 0.601 AC: 91069 AN: 151644 Hom.: 30948 Cov.: 31

Gnomad AFR AF: 0.271

Gnomad AMI AF: 0.890

Gnomad AMR AF: 0.663

Gnomad ASJ AF: 0.832

Gnomad EAS AF: 0.407

Gnomad SAS AF: 0.658

Gnomad FIN AF: 0.703

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.764

Gnomad OTH AF: 0.655

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

GnomAD4 genome AF: 0.600 AC: 91099 AN: 151762 Hom.: 30958 Cov.: 31 AF XY: 0.598 AC XY: 44285 AN XY: 74112

African (AFR) AF: 0.270 AC: 11165 AN: 41316

American (AMR) AF: 0.663 AC: 10128 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.832 AC: 2881 AN: 3464

East Asian (EAS) AF: 0.408 AC: 2099 AN: 5148

South Asian (SAS) AF: 0.659 AC: 3161 AN: 4800

European-Finnish (FIN) AF: 0.703 AC: 7390 AN: 10506

Middle Eastern (MID) AF: 0.646 AC: 190 AN: 294

European-Non Finnish (NFE) AF: 0.764 AC: 51891 AN: 67948

Other (OTH) AF: 0.656 AC: 1382 AN: 2108

Alfa AF: 0.713 Hom.: 170542

Bravo AF: 0.579

Asia WGS AF: 0.566 AC: 1967 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.7
DANN	Benign	0.42
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs7746680; hg19: chr6-45777347;