rs737366

chr2-64807060-A-Cchr2-64807060-A-Gchr2-64807060-A-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 0.902 in 150,594 control chromosomes in the GnomAD database, including 61,050 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 0.90 (61050 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.07

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.942 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: 0.902 AC: 135727 AN: 150478 Hom.: 61006 Cov.: 28

Gnomad AFR AF: 0.884

Gnomad AMI AF: 0.840

Gnomad AMR AF: 0.936

Gnomad ASJ AF: 0.961

Gnomad EAS AF: 0.898

Gnomad SAS AF: 0.966

Gnomad FIN AF: 0.846

Gnomad MID AF: 0.940

Gnomad NFE AF: 0.907

Gnomad OTH AF: 0.924

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

GnomAD4 genome AF: 0.902 AC: 135827 AN: 150594 Hom.: 61050 Cov.: 28 AF XY: 0.901 AC XY: 66225 AN XY: 73526

Gnomad4 AFR AF: 0.883

Gnomad4 AMR AF: 0.936

Gnomad4 ASJ AF: 0.961

Gnomad4 EAS AF: 0.898

Gnomad4 SAS AF: 0.966

Gnomad4 FIN AF: 0.846

Gnomad4 NFE AF: 0.907

Gnomad4 OTH AF: 0.925

Alfa AF: 0.912 Hom.: 3981

Bravo AF: 0.902

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.14
Dann	Benign	0.14

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs737366; hg19: chr2-65034194;