rs6731600

chr2-27308797-T-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 0.0511 in 152,204 control chromosomes in the GnomAD database, including 260 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 0.051 (260 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.00

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0872 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: 0.0512 AC: 7780 AN: 152086 Hom.: 260 Cov.: 32

Gnomad AFR AF: 0.0900

Gnomad AMI AF: 0.110

Gnomad AMR AF: 0.0426

Gnomad ASJ AF: 0.0248

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.0559

Gnomad FIN AF: 0.0154

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0391

Gnomad OTH AF: 0.0526

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

GnomAD4 genome AF: 0.0511 AC: 7775 AN: 152204 Hom.: 260 Cov.: 32 AF XY: 0.0486 AC XY: 3616 AN XY: 74412

Gnomad4 AFR AF: 0.0896

Gnomad4 AMR AF: 0.0425

Gnomad4 ASJ AF: 0.0248

Gnomad4 EAS AF: 0.000772

Gnomad4 SAS AF: 0.0564

Gnomad4 FIN AF: 0.0154

Gnomad4 NFE AF: 0.0391

Gnomad4 OTH AF: 0.0521

Alfa AF: 0.0419 Hom.: 140

Bravo AF: 0.0547

Asia WGS AF: 0.0230 AC: 81 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	12
Dann	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6731600; hg19: chr2-27531665;