2-4271386-T-C

Position:

• chr2-4271386-T-C

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 0.113 in 152,000 control chromosomes in the GnomAD database, including 1,039 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 0.11 (1039 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.742

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.138 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: 0.114 AC: 17249 AN: 151882 Hom.: 1038 Cov.: 31

Gnomad AFR AF: 0.0937

Gnomad AMI AF: 0.156

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.159

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.0801

Gnomad FIN AF: 0.0819

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.141

Gnomad OTH AF: 0.103

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

GnomAD4 genome AF: 0.113 AC: 17251 AN: 152000 Hom.: 1039 Cov.: 31 AF XY: 0.110 AC XY: 8196 AN XY: 74322

Gnomad4 AFR AF: 0.0937

Gnomad4 AMR AF: 0.106

Gnomad4 ASJ AF: 0.159

Gnomad4 EAS AF: 0.00154

Gnomad4 SAS AF: 0.0797

Gnomad4 FIN AF: 0.0819

Gnomad4 NFE AF: 0.140

Gnomad4 OTH AF: 0.102

Alfa AF: 0.135 Hom.: 1292

Bravo AF: 0.112

Asia WGS AF: 0.0390 AC: 135 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	11
DANN	Benign	0.89

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11686135; hg19: chr2-4318976;