rs4131366

Positions:

• chr2-44010648-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 0.103 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;