rs10146615

Variant names:

• chr14-62265946-T-C
• rs10146615

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.262 in 152,072 control chromosomes in the GnomAD database, including 5,912 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 0.26 (5912 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.159
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.42).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.387 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: 0.262 AC: 39862 AN: 151954 Hom.: 5913 Cov.: 32

Gnomad AFR AF: 0.392

Gnomad AMI AF: 0.220

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.277

Gnomad EAS AF: 0.00732

Gnomad SAS AF: 0.213

Gnomad FIN AF: 0.199

Gnomad MID AF: 0.303

Gnomad NFE AF: 0.235

Gnomad OTH AF: 0.262

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

GnomAD4 genome AF: 0.262 AC: 39877 AN: 152072 Hom.: 5912 Cov.: 32 AF XY: 0.255 AC XY: 18995 AN XY: 74354

African (AFR) AF: 0.392 AC: 16255 AN: 41472

American (AMR) AF: 0.178 AC: 2715 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.277 AC: 960 AN: 3470

East Asian (EAS) AF: 0.00753 AC: 39 AN: 5182

South Asian (SAS) AF: 0.212 AC: 1024 AN: 4826

European-Finnish (FIN) AF: 0.199 AC: 2103 AN: 10584

Middle Eastern (MID) AF: 0.308 AC: 90 AN: 292

European-Non Finnish (NFE) AF: 0.235 AC: 15945 AN: 67952

Other (OTH) AF: 0.259 AC: 546 AN: 2112

Alfa AF: 0.244 Hom.: 16292

Bravo AF: 0.265

Asia WGS AF: 0.112 AC: 389 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.42
CADD	Benign	12
DANN	Benign	0.71
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs10146615; hg19: chr14-62732664;