rs10506347

Variant names:

• chr12-56937303-T-C
• rs10506347

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 0.129 in 152,040 control chromosomes in the GnomAD database, including 1,325 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 0.13 (1325 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0570
• Publications: 10 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 = 0.209 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: 0.129 AC: 19582 AN: 151922 Hom.: 1330 Cov.: 31

Gnomad AFR AF: 0.167

Gnomad AMI AF: 0.0746

Gnomad AMR AF: 0.141

Gnomad ASJ AF: 0.135

Gnomad EAS AF: 0.220

Gnomad SAS AF: 0.125

Gnomad FIN AF: 0.109

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.114

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

GnomAD4 genome AF: 0.129 AC: 19588 AN: 152040 Hom.: 1325 Cov.: 31 AF XY: 0.130 AC XY: 9648 AN XY: 74324

African (AFR) AF: 0.166 AC: 6897 AN: 41448

American (AMR) AF: 0.141 AC: 2150 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.135 AC: 470 AN: 3472

East Asian (EAS) AF: 0.219 AC: 1130 AN: 5156

South Asian (SAS) AF: 0.125 AC: 602 AN: 4810

European-Finnish (FIN) AF: 0.109 AC: 1158 AN: 10600

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

European-Non Finnish (NFE) AF: 0.101 AC: 6854 AN: 67960

Other (OTH) AF: 0.114 AC: 241 AN: 2110

Alfa AF: 0.109 Hom.: 1620

Bravo AF: 0.132

Asia WGS AF: 0.162 AC: 562 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	5.4
DANN	Benign	0.39
PhyloP100		-0.057

Splicing

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

Other links and lift over

dbSNP: rs10506347; hg19: chr12-57331087;