rs2709736

chr7-20822683-C-T

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 0.508 in 152,022 control chromosomes in the GnomAD database, including 20,557 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 (20557 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.163

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.672 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.507 AC: 77060 AN: 151904 Hom.: 20521 Cov.: 33

Gnomad AFR AF: 0.679

Gnomad AMI AF: 0.609

Gnomad AMR AF: 0.458

Gnomad ASJ AF: 0.449

Gnomad EAS AF: 0.376

Gnomad SAS AF: 0.417

Gnomad FIN AF: 0.381

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.453

Gnomad OTH AF: 0.485

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

GnomAD4 genome AF: 0.508 AC: 77154 AN: 152022 Hom.: 20557 Cov.: 33 AF XY: 0.501 AC XY: 37200 AN XY: 74312

Gnomad4 AFR AF: 0.679

Gnomad4 AMR AF: 0.458

Gnomad4 ASJ AF: 0.449

Gnomad4 EAS AF: 0.377

Gnomad4 SAS AF: 0.416

Gnomad4 FIN AF: 0.381

Gnomad4 NFE AF: 0.453

Gnomad4 OTH AF: 0.484

Alfa AF: 0.460 Hom.: 25588

Bravo AF: 0.522

Asia WGS AF: 0.388 AC: 1351 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	3.6
Dann	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2709736; hg19: chr7-20862302;