rs2430692

Variant names:

• chr12-14912889-A-G
• rs2430692

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 0.463 in 151,998 control chromosomes in the GnomAD database, including 17,336 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 0.46 (17336 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0740
• Publications: 15 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.624 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: 0.463 AC: 70308 AN: 151880 Hom.: 17301 Cov.: 32

Gnomad AFR AF: 0.630

Gnomad AMI AF: 0.579

Gnomad AMR AF: 0.432

Gnomad ASJ AF: 0.442

Gnomad EAS AF: 0.177

Gnomad SAS AF: 0.407

Gnomad FIN AF: 0.362

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.409

Gnomad OTH AF: 0.470

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

GnomAD4 genome AF: 0.463 AC: 70389 AN: 151998 Hom.: 17336 Cov.: 32 AF XY: 0.458 AC XY: 33989 AN XY: 74288

African (AFR) AF: 0.630 AC: 26108 AN: 41418

American (AMR) AF: 0.432 AC: 6598 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.442 AC: 1534 AN: 3472

East Asian (EAS) AF: 0.176 AC: 910 AN: 5170

South Asian (SAS) AF: 0.408 AC: 1965 AN: 4818

European-Finnish (FIN) AF: 0.362 AC: 3822 AN: 10552

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.409 AC: 27810 AN: 67976

Other (OTH) AF: 0.467 AC: 988 AN: 2114

Alfa AF: 0.434 Hom.: 40281

Bravo AF: 0.472

Asia WGS AF: 0.330 AC: 1151 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.6
DANN	Benign	0.38
PhyloP100		0.074

Splicing

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

Other links and lift over

dbSNP: rs2430692; hg19: chr12-15065823;