rs6737562

Variant names:

• chr2-179363665-T-G
• rs6737562

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 0.0744 in 152,280 control chromosomes in the GnomAD database, including 522 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 0.074 (522 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.558

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.101 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: 0.0743 AC: 11313 AN: 152162 Hom.: 518 Cov.: 32

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.277

Gnomad AMR AF: 0.0493

Gnomad ASJ AF: 0.0642

Gnomad EAS AF: 0.000384

Gnomad SAS AF: 0.0228

Gnomad FIN AF: 0.0819

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0684

Gnomad OTH AF: 0.0718

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

GnomAD4 genome AF: 0.0744 AC: 11326 AN: 152280 Hom.: 522 Cov.: 32 AF XY: 0.0730 AC XY: 5439 AN XY: 74458

Gnomad4 AFR AF: 0.103

Gnomad4 AMR AF: 0.0492

Gnomad4 ASJ AF: 0.0642

Gnomad4 EAS AF: 0.000385

Gnomad4 SAS AF: 0.0226

Gnomad4 FIN AF: 0.0819

Gnomad4 NFE AF: 0.0685

Gnomad4 OTH AF: 0.0710

Alfa AF: 0.0695 Hom.: 188

Bravo AF: 0.0729

Asia WGS AF: 0.0170 AC: 59 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.4
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6737562; hg19: chr2-180228392;