rs12415607

Variant names:

• chr10-113678445-C-A
• rs12415607

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 0.221 in 152,082 control chromosomes in the GnomAD database, including 3,993 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 0.22 (3993 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0190
• Publications: 25 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 = 0.407 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: 0.221 AC: 33600 AN: 151964 Hom.: 3986 Cov.: 32

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.387

Gnomad AMR AF: 0.250

Gnomad ASJ AF: 0.146

Gnomad EAS AF: 0.422

Gnomad SAS AF: 0.289

Gnomad FIN AF: 0.261

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.226

Gnomad OTH AF: 0.236

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

GnomAD4 genome AF: 0.221 AC: 33628 AN: 152082 Hom.: 3993 Cov.: 32 AF XY: 0.226 AC XY: 16784 AN XY: 74334

African (AFR) AF: 0.160 AC: 6651 AN: 41474

American (AMR) AF: 0.250 AC: 3828 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.146 AC: 508 AN: 3472

East Asian (EAS) AF: 0.421 AC: 2182 AN: 5180

South Asian (SAS) AF: 0.289 AC: 1390 AN: 4816

European-Finnish (FIN) AF: 0.261 AC: 2753 AN: 10558

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.226 AC: 15384 AN: 67980

Other (OTH) AF: 0.238 AC: 502 AN: 2110

Alfa AF: 0.227 Hom.: 8509

Bravo AF: 0.218

Asia WGS AF: 0.321 AC: 1116 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	0.65
DANN	Benign	0.52
PhyloP100		0.019

Splicing

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

Other links and lift over

dbSNP: rs12415607; hg19: chr10-115438204;