2-170141311-G-T

Variant names:

• chr2-170141311-G-T
• rs13414831

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 0.317 in 152,030 control chromosomes in the GnomAD database, including 7,886 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 0.32 (7886 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.542
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.519 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.317 AC: 48179 AN: 151912 Hom.: 7879 Cov.: 32

Gnomad AFR AF: 0.302

Gnomad AMI AF: 0.379

Gnomad AMR AF: 0.320

Gnomad ASJ AF: 0.408

Gnomad EAS AF: 0.536

Gnomad SAS AF: 0.398

Gnomad FIN AF: 0.353

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.292

Gnomad OTH AF: 0.317

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

GnomAD4 genome AF: 0.317 AC: 48227 AN: 152030 Hom.: 7886 Cov.: 32 AF XY: 0.322 AC XY: 23895 AN XY: 74320

African (AFR) AF: 0.302 AC: 12526 AN: 41478

American (AMR) AF: 0.320 AC: 4887 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.408 AC: 1415 AN: 3468

East Asian (EAS) AF: 0.535 AC: 2752 AN: 5140

South Asian (SAS) AF: 0.398 AC: 1915 AN: 4814

European-Finnish (FIN) AF: 0.353 AC: 3727 AN: 10570

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.292 AC: 19866 AN: 67958

Other (OTH) AF: 0.321 AC: 679 AN: 2116

Alfa AF: 0.304 Hom.: 9214

Bravo AF: 0.313

Asia WGS AF: 0.460 AC: 1597 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	5.2
DANN	Benign	0.85
PhyloP100		0.54

Splicing

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

Other links and lift over

dbSNP: rs13414831; hg19: chr2-170997821;