rs12413624

Variant names:

• chr10-118519432-T-A
• rs12413624

Your query was ambiguous. Multiple possible variants found:

• chr10-118519432-T-A
• chr10-118519432-T-C

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 0.345 in 152,108 control chromosomes in the GnomAD database, including 10,371 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 0.34 (10371 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.25
• Publications: 29 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.435 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: 0.345 AC: 52393 AN: 151990 Hom.: 10365 Cov.: 32

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.255

Gnomad AMR AF: 0.417

Gnomad ASJ AF: 0.318

Gnomad EAS AF: 0.380

Gnomad SAS AF: 0.320

Gnomad FIN AF: 0.443

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.439

Gnomad OTH AF: 0.352

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

GnomAD4 genome AF: 0.345 AC: 52420 AN: 152108 Hom.: 10371 Cov.: 32 AF XY: 0.347 AC XY: 25778 AN XY: 74346

African (AFR) AF: 0.140 AC: 5815 AN: 41520

American (AMR) AF: 0.418 AC: 6387 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.318 AC: 1102 AN: 3470

East Asian (EAS) AF: 0.380 AC: 1960 AN: 5156

South Asian (SAS) AF: 0.321 AC: 1545 AN: 4818

European-Finnish (FIN) AF: 0.443 AC: 4681 AN: 10564

Middle Eastern (MID) AF: 0.395 AC: 116 AN: 294

European-Non Finnish (NFE) AF: 0.439 AC: 29844 AN: 67984

Other (OTH) AF: 0.350 AC: 737 AN: 2106

Alfa AF: 0.385 Hom.: 1568

Bravo AF: 0.338

Asia WGS AF: 0.335 AC: 1165 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	12
DANN	Benign	0.73
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs12413624; hg19: chr10-120278944;