rs4143271

Positions:

• chr2-37796082-G-A
• chr2-37796082-G-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.0956 in 152,130 control chromosomes in the GnomAD database, including 932 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 0.096 (932 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.74

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.39).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.276 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: 0.0957 AC: 14550 AN: 152012 Hom.: 932 Cov.: 32

Gnomad AFR AF: 0.0292

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.123

Gnomad EAS AF: 0.287

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.103

Gnomad OTH AF: 0.0944

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

GnomAD4 genome AF: 0.0956 AC: 14547 AN: 152130 Hom.: 932 Cov.: 32 AF XY: 0.101 AC XY: 7499 AN XY: 74360

Gnomad4 AFR AF: 0.0291

Gnomad4 AMR AF: 0.114

Gnomad4 ASJ AF: 0.123

Gnomad4 EAS AF: 0.288

Gnomad4 SAS AF: 0.145

Gnomad4 FIN AF: 0.153

Gnomad4 NFE AF: 0.103

Gnomad4 OTH AF: 0.0935

Alfa AF: 0.0978 Hom.: 138

Bravo AF: 0.0890

Asia WGS AF: 0.190 AC: 661 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.39
CADD	Benign	17
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4143271; hg19: chr2-38023225;