chr2-23315972-T-G

Variant names:

• chr2-23315972-T-G
• rs1002158

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 0.705 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.705 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

Gnomad4 AFR AF: 0.586

Gnomad4 AMR AF: 0.770

Gnomad4 ASJ AF: 0.735

Gnomad4 EAS AF: 0.601

Gnomad4 SAS AF: 0.851

Gnomad4 FIN AF: 0.776

Gnomad4 NFE AF: 0.747

Gnomad4 OTH AF: 0.729

Alfa AF: 0.735 Hom.: 54369

Bravo AF: 0.693

Asia WGS AF: 0.764 AC: 2657 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1002158; hg19: chr2-23538843;