rs1374441

Variant names:

• chr2-148801056-G-A
• rs1374441

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.823 AC: 34146 AN: 41504

American (AMR) AF: 0.645 AC: 9857 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.802 AC: 2783 AN: 3470

East Asian (EAS) AF: 0.541 AC: 2794 AN: 5162

South Asian (SAS) AF: 0.582 AC: 2808 AN: 4822

European-Finnish (FIN) AF: 0.768 AC: 8136 AN: 10588

Middle Eastern (MID) AF: 0.839 AC: 245 AN: 292

European-Non Finnish (NFE) AF: 0.798 AC: 54255 AN: 68014

Other (OTH) AF: 0.776 AC: 1637 AN: 2110

Alfa AF: 0.785 Hom.: 148732

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
PhyloP100		-0.94

Splicing

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

Other links and lift over

dbSNP: rs1374441; hg19: chr2-149558625;