rs2709748

Variant names:

• chr7-20780150-G-A
• rs2709748

Your query was ambiguous. Multiple possible variants found:

• chr7-20780150-G-A
• chr7-20780150-G-C

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 0.196 in 152,154 control chromosomes in the GnomAD database, including 3,763 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 0.20 (3763 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0370
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.339 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: 0.196 AC: 29742 AN: 152038 Hom.: 3759 Cov.: 33

Gnomad AFR AF: 0.344

Gnomad AMI AF: 0.0899

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.110

Gnomad EAS AF: 0.322

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.121

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.124

Gnomad OTH AF: 0.189

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

GnomAD4 genome AF: 0.196 AC: 29779 AN: 152154 Hom.: 3763 Cov.: 33 AF XY: 0.195 AC XY: 14477 AN XY: 74398

African (AFR) AF: 0.343 AC: 14242 AN: 41468

American (AMR) AF: 0.180 AC: 2748 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.110 AC: 381 AN: 3472

East Asian (EAS) AF: 0.321 AC: 1660 AN: 5170

South Asian (SAS) AF: 0.103 AC: 499 AN: 4828

European-Finnish (FIN) AF: 0.121 AC: 1277 AN: 10584

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.124 AC: 8440 AN: 68020

Other (OTH) AF: 0.192 AC: 406 AN: 2110

Alfa AF: 0.148 Hom.: 4902

Bravo AF: 0.205

Asia WGS AF: 0.245 AC: 847 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	7.6
DANN	Benign	0.78
PhyloP100		-0.037

Splicing

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

Other links and lift over

dbSNP: rs2709748; hg19: chr7-20819770;