rs2782660

Variant names:

• chr6-45719596-A-G
• rs2782660

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 0.511 in 152,040 control chromosomes in the GnomAD database, including 22,916 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 0.51 (22916 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.74
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.663 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: 0.511 AC: 77643 AN: 151922 Hom.: 22923 Cov.: 32

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.564

Gnomad AMR AF: 0.502

Gnomad ASJ AF: 0.694

Gnomad EAS AF: 0.340

Gnomad SAS AF: 0.621

Gnomad FIN AF: 0.646

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.668

Gnomad OTH AF: 0.539

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

GnomAD4 genome AF: 0.511 AC: 77633 AN: 152040 Hom.: 22916 Cov.: 32 AF XY: 0.509 AC XY: 37818 AN XY: 74318

African (AFR) AF: 0.211 AC: 8752 AN: 41494

American (AMR) AF: 0.501 AC: 7664 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.694 AC: 2408 AN: 3472

East Asian (EAS) AF: 0.340 AC: 1757 AN: 5166

South Asian (SAS) AF: 0.621 AC: 2992 AN: 4816

European-Finnish (FIN) AF: 0.646 AC: 6821 AN: 10554

Middle Eastern (MID) AF: 0.653 AC: 192 AN: 294

European-Non Finnish (NFE) AF: 0.668 AC: 45399 AN: 67944

Other (OTH) AF: 0.539 AC: 1134 AN: 2104

Alfa AF: 0.623 Hom.: 131378

Bravo AF: 0.488

Asia WGS AF: 0.458 AC: 1592 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	7.0
DANN	Benign	0.55
PhyloP100		1.7

Splicing

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

Other links and lift over

dbSNP: rs2782660; hg19: chr6-45687333;