rs2373461

Variant names:

• chr12-101559943-G-T
• rs2373461

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 0.0447 in 151,824 control chromosomes in the GnomAD database, including 160 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 0.045 (160 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.171
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0511 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: 0.0447 AC: 6786 AN: 151706 Hom.: 160 Cov.: 32

Gnomad AFR AF: 0.0372

Gnomad AMI AF: 0.0484

Gnomad AMR AF: 0.0342

Gnomad ASJ AF: 0.0295

Gnomad EAS AF: 0.0536

Gnomad SAS AF: 0.0322

Gnomad FIN AF: 0.0449

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0525

Gnomad OTH AF: 0.0446

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

GnomAD4 genome AF: 0.0447 AC: 6790 AN: 151824 Hom.: 160 Cov.: 32 AF XY: 0.0438 AC XY: 3258 AN XY: 74340

African (AFR) AF: 0.0372 AC: 1543 AN: 41472

American (AMR) AF: 0.0342 AC: 522 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.0295 AC: 102 AN: 3456

East Asian (EAS) AF: 0.0535 AC: 276 AN: 5156

South Asian (SAS) AF: 0.0331 AC: 159 AN: 4804

European-Finnish (FIN) AF: 0.0449 AC: 476 AN: 10606

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0525 AC: 3557 AN: 67756

Other (OTH) AF: 0.0441 AC: 93 AN: 2108

Alfa AF: 0.0459 Hom.: 57

Bravo AF: 0.0441

Asia WGS AF: 0.0490 AC: 171 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.0
DANN	Benign	0.34
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs2373461; hg19: chr12-101953721;