rs1374441

Positions:

• chr2-148801056-G-A

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 0.771 in 152,164 control chromosomes in the GnomAD database, including 45,745 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 0.77 (45745 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.941

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.815 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: 0.771 AC: 117216 AN: 152048 Hom.: 45715 Cov.: 32

Gnomad AFR AF: 0.823

Gnomad AMI AF: 0.689

Gnomad AMR AF: 0.645

Gnomad ASJ AF: 0.802

Gnomad EAS AF: 0.542

Gnomad SAS AF: 0.582

Gnomad FIN AF: 0.768

Gnomad MID AF: 0.834

Gnomad NFE AF: 0.798

Gnomad OTH AF: 0.782

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

GnomAD4 genome AF: 0.771 AC: 117289 AN: 152164 Hom.: 45745 Cov.: 32 AF XY: 0.762 AC XY: 56725 AN XY: 74394

Gnomad4 AFR AF: 0.823

Gnomad4 AMR AF: 0.645

Gnomad4 ASJ AF: 0.802

Gnomad4 EAS AF: 0.541

Gnomad4 SAS AF: 0.582

Gnomad4 FIN AF: 0.768

Gnomad4 NFE AF: 0.798

Gnomad4 OTH AF: 0.776

Alfa AF: 0.785 Hom.: 95069

Bravo AF: 0.764

Asia WGS AF: 0.572 AC: 1992 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	0.55
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1374441; hg19: chr2-149558625;