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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.343

Gnomad4 AMR AF: 0.180

Gnomad4 ASJ AF: 0.110

Gnomad4 EAS AF: 0.321

Gnomad4 SAS AF: 0.103

Gnomad4 FIN AF: 0.121

Gnomad4 NFE AF: 0.124

Gnomad4 OTH AF: 0.192

Alfa AF: 0.133 Hom.: 1125

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2709748; hg19: chr7-20819770;