rs1137

Positions:

• chr2-74712049-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 0.595 in 152,146 control chromosomes in the GnomAD database, including 32,467 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 0.59 (32467 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.899

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.79 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.595 AC: 90512 AN: 152028 Hom.: 32469 Cov.: 31

Gnomad AFR AF: 0.202

Gnomad AMI AF: 0.706

Gnomad AMR AF: 0.684

Gnomad ASJ AF: 0.836

Gnomad EAS AF: 0.176

Gnomad SAS AF: 0.646

Gnomad FIN AF: 0.791

Gnomad MID AF: 0.769

Gnomad NFE AF: 0.796

Gnomad OTH AF: 0.668

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

GnomAD4 genome AF: 0.595 AC: 90524 AN: 152146 Hom.: 32467 Cov.: 31 AF XY: 0.595 AC XY: 44231 AN XY: 74380

Gnomad4 AFR AF: 0.201

Gnomad4 AMR AF: 0.684

Gnomad4 ASJ AF: 0.836

Gnomad4 EAS AF: 0.176

Gnomad4 SAS AF: 0.645

Gnomad4 FIN AF: 0.791

Gnomad4 NFE AF: 0.796

Gnomad4 OTH AF: 0.669

Alfa AF: 0.758 Hom.: 51559

Bravo AF: 0.567

Asia WGS AF: 0.417 AC: 1451 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.60
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1137; hg19: chr2-74939176;