rs4131366

Variant names:

• chr2-44010648-G-A
• rs4131366

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 0.103 in 152,098 control chromosomes in the GnomAD database, including 924 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 0.10 (924 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.944

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.136 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: 0.102 AC: 15575 AN: 151980 Hom.: 924 Cov.: 32

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.0603

Gnomad ASJ AF: 0.120

Gnomad EAS AF: 0.00924

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.0739

Gnomad MID AF: 0.124

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.0913

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

GnomAD4 genome AF: 0.103 AC: 15592 AN: 152098 Hom.: 924 Cov.: 32 AF XY: 0.102 AC XY: 7597 AN XY: 74370

Gnomad4 AFR AF: 0.126

Gnomad4 AMR AF: 0.0603

Gnomad4 ASJ AF: 0.120

Gnomad4 EAS AF: 0.00926

Gnomad4 SAS AF: 0.145

Gnomad4 FIN AF: 0.0739

Gnomad4 NFE AF: 0.105

Gnomad4 OTH AF: 0.0903

Alfa AF: 0.106 Hom.: 1242

Bravo AF: 0.100

Asia WGS AF: 0.0640 AC: 224 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	1.8
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4131366; hg19: chr2-44237787;