rs10876447

Variant names:

• chr12-53377157-G-A
• rs10876447

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 0.157 in 152,134 control chromosomes in the GnomAD database, including 1,967 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 0.16 (1967 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.493
• Publications: 18 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.187 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: 0.157 AC: 23869 AN: 152016 Hom.: 1964 Cov.: 32

Gnomad AFR AF: 0.159

Gnomad AMI AF: 0.165

Gnomad AMR AF: 0.192

Gnomad ASJ AF: 0.117

Gnomad EAS AF: 0.196

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.140

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

GnomAD4 genome AF: 0.157 AC: 23887 AN: 152134 Hom.: 1967 Cov.: 32 AF XY: 0.157 AC XY: 11673 AN XY: 74370

African (AFR) AF: 0.159 AC: 6595 AN: 41520

American (AMR) AF: 0.193 AC: 2943 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.117 AC: 405 AN: 3472

East Asian (EAS) AF: 0.196 AC: 1013 AN: 5174

South Asian (SAS) AF: 0.146 AC: 704 AN: 4816

European-Finnish (FIN) AF: 0.123 AC: 1298 AN: 10584

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.154 AC: 10463 AN: 67988

Other (OTH) AF: 0.138 AC: 291 AN: 2110

Alfa AF: 0.154 Hom.: 3188

Bravo AF: 0.159

Asia WGS AF: 0.149 AC: 515 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	17
DANN	Benign	0.62
PhyloP100		0.49

Splicing

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

Other links and lift over

dbSNP: rs10876447; hg19: chr12-53770941;