2-156377320-C-G

Variant names:

• chr2-156377320-C-G
• rs1405735

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.602 AC: 24949 AN: 41478

American (AMR) AF: 0.764 AC: 11680 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.706 AC: 2451 AN: 3472

East Asian (EAS) AF: 0.765 AC: 3970 AN: 5188

South Asian (SAS) AF: 0.817 AC: 3946 AN: 4830

European-Finnish (FIN) AF: 0.747 AC: 7917 AN: 10594

Middle Eastern (MID) AF: 0.786 AC: 231 AN: 294

European-Non Finnish (NFE) AF: 0.753 AC: 51250 AN: 68018

Other (OTH) AF: 0.698 AC: 1473 AN: 2110

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
PhyloP100		-2.6

Splicing

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

Other links and lift over

dbSNP: rs1405735; hg19: chr2-157233832;