rs10514613

Variant names:

• chr16-86096925-T-C
• rs10514613

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 0.0905 in 152,228 control chromosomes in the GnomAD database, including 1,015 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 0.091 (1015 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.599
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.238 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: 0.0904 AC: 13757 AN: 152110 Hom.: 1007 Cov.: 33

Gnomad AFR AF: 0.0747

Gnomad AMI AF: 0.0154

Gnomad AMR AF: 0.239

Gnomad ASJ AF: 0.0945

Gnomad EAS AF: 0.249

Gnomad SAS AF: 0.0832

Gnomad FIN AF: 0.0981

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0556

Gnomad OTH AF: 0.0726

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

GnomAD4 genome AF: 0.0905 AC: 13781 AN: 152228 Hom.: 1015 Cov.: 33 AF XY: 0.0964 AC XY: 7172 AN XY: 74410

African (AFR) AF: 0.0748 AC: 3105 AN: 41536

American (AMR) AF: 0.240 AC: 3663 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0945 AC: 328 AN: 3472

East Asian (EAS) AF: 0.249 AC: 1290 AN: 5176

South Asian (SAS) AF: 0.0832 AC: 400 AN: 4806

European-Finnish (FIN) AF: 0.0981 AC: 1040 AN: 10606

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0556 AC: 3783 AN: 68026

Other (OTH) AF: 0.0718 AC: 152 AN: 2116

Alfa AF: 0.0756 Hom.: 429

Bravo AF: 0.103

Asia WGS AF: 0.142 AC: 493 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.27
DANN	Benign	0.71
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs10514613; hg19: chr16-86130531;