2-156377320-C-G

Variant names:

• chr2-156377320-C-G
• rs1405735

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 0.713 in 152,190 control chromosomes in the GnomAD database, including 39,131 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 0.71 (39131 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.64

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.796 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: 0.714 AC: 108507 AN: 152070 Hom.: 39113 Cov.: 33

Gnomad AFR AF: 0.602

Gnomad AMI AF: 0.766

Gnomad AMR AF: 0.763

Gnomad ASJ AF: 0.706

Gnomad EAS AF: 0.764

Gnomad SAS AF: 0.818

Gnomad FIN AF: 0.747

Gnomad MID AF: 0.785

Gnomad NFE AF: 0.753

Gnomad OTH AF: 0.700

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

GnomAD4 genome AF: 0.713 AC: 108566 AN: 152190 Hom.: 39131 Cov.: 33 AF XY: 0.714 AC XY: 53139 AN XY: 74408

Gnomad4 AFR AF: 0.602

Gnomad4 AMR AF: 0.764

Gnomad4 ASJ AF: 0.706

Gnomad4 EAS AF: 0.765

Gnomad4 SAS AF: 0.817

Gnomad4 FIN AF: 0.747

Gnomad4 NFE AF: 0.753

Gnomad4 OTH AF: 0.698

Alfa AF: 0.626 Hom.: 1809

Bravo AF: 0.706

Asia WGS AF: 0.724 AC: 2514 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.12
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1405735; hg19: chr2-157233832;