chr2-42115839-C-T

Variant names:

• chr2-42115839-C-T
• rs1530163

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 0.295 in 152,066 control chromosomes in the GnomAD database, including 6,681 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 0.30 (6681 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.32
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.366 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.295 AC: 44883 AN: 151948 Hom.: 6669 Cov.: 31

Gnomad AFR AF: 0.321

Gnomad AMI AF: 0.152

Gnomad AMR AF: 0.243

Gnomad ASJ AF: 0.304

Gnomad EAS AF: 0.228

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.323

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.288

Gnomad OTH AF: 0.288

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

GnomAD4 genome AF: 0.295 AC: 44919 AN: 152066 Hom.: 6681 Cov.: 31 AF XY: 0.296 AC XY: 21978 AN XY: 74320

African (AFR) AF: 0.321 AC: 13316 AN: 41470

American (AMR) AF: 0.242 AC: 3703 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.304 AC: 1056 AN: 3468

East Asian (EAS) AF: 0.229 AC: 1183 AN: 5170

South Asian (SAS) AF: 0.381 AC: 1833 AN: 4814

European-Finnish (FIN) AF: 0.323 AC: 3413 AN: 10560

Middle Eastern (MID) AF: 0.300 AC: 87 AN: 290

European-Non Finnish (NFE) AF: 0.288 AC: 19575 AN: 67994

Other (OTH) AF: 0.292 AC: 615 AN: 2108

Alfa AF: 0.297 Hom.: 4794

Bravo AF: 0.285

Asia WGS AF: 0.298 AC: 1038 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	7.9
DANN	Benign	0.71
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs1530163; hg19: chr2-42342979;