chr2-23315972-T-G

Variant names:

• chr2-23315972-T-G
• rs1002158

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 0.705 in 152,024 control chromosomes in the GnomAD database, including 38,243 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 0.70 (38243 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0140
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.83 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.705 AC: 107073 AN: 151906 Hom.: 38232 Cov.: 32

Gnomad AFR AF: 0.587

Gnomad AMI AF: 0.592

Gnomad AMR AF: 0.770

Gnomad ASJ AF: 0.735

Gnomad EAS AF: 0.602

Gnomad SAS AF: 0.852

Gnomad FIN AF: 0.776

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.748

Gnomad OTH AF: 0.726

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

GnomAD4 genome AF: 0.705 AC: 107112 AN: 152024 Hom.: 38243 Cov.: 32 AF XY: 0.708 AC XY: 52636 AN XY: 74328

African (AFR) AF: 0.586 AC: 24292 AN: 41428

American (AMR) AF: 0.770 AC: 11773 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.735 AC: 2552 AN: 3472

East Asian (EAS) AF: 0.601 AC: 3101 AN: 5158

South Asian (SAS) AF: 0.851 AC: 4097 AN: 4812

European-Finnish (FIN) AF: 0.776 AC: 8204 AN: 10576

Middle Eastern (MID) AF: 0.704 AC: 207 AN: 294

European-Non Finnish (NFE) AF: 0.747 AC: 50808 AN: 67974

Other (OTH) AF: 0.729 AC: 1539 AN: 2110

Alfa AF: 0.730 Hom.: 74538

Bravo AF: 0.693

Asia WGS AF: 0.764 AC: 2657 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.3
DANN	Benign	0.73
PhyloP100		-0.014

Splicing

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

Other links and lift over

dbSNP: rs1002158; hg19: chr2-23538843;