rs10506698

Variant names:

• chr12-74651637-T-C
• rs10506698

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 0.078 in 152,286 control chromosomes in the GnomAD database, including 605 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 0.078 (605 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.283
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.112 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: 0.0779 AC: 11858 AN: 152168 Hom.: 604 Cov.: 32

Gnomad AFR AF: 0.0321

Gnomad AMI AF: 0.0570

Gnomad AMR AF: 0.0504

Gnomad ASJ AF: 0.0767

Gnomad EAS AF: 0.0210

Gnomad SAS AF: 0.0352

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.114

Gnomad OTH AF: 0.0621

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

GnomAD4 genome AF: 0.0780 AC: 11871 AN: 152286 Hom.: 605 Cov.: 32 AF XY: 0.0766 AC XY: 5702 AN XY: 74462

African (AFR) AF: 0.0322 AC: 1339 AN: 41576

American (AMR) AF: 0.0502 AC: 768 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0767 AC: 266 AN: 3470

East Asian (EAS) AF: 0.0210 AC: 109 AN: 5186

South Asian (SAS) AF: 0.0354 AC: 171 AN: 4828

European-Finnish (FIN) AF: 0.117 AC: 1236 AN: 10602

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.114 AC: 7772 AN: 68016

Other (OTH) AF: 0.0662 AC: 140 AN: 2114

Alfa AF: 0.0936 Hom.: 134

Bravo AF: 0.0704

Asia WGS AF: 0.0440 AC: 154 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.9
DANN	Benign	0.68
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs10506698; hg19: chr12-75045417;