rs12769316

Variant names:

• chr10-102392994-G-A
• rs12769316

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 0.131 in 152,084 control chromosomes in the GnomAD database, including 1,585 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 (1585 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.352
• Publications: 16 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.176 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: 0.131 AC: 19969 AN: 151966 Hom.: 1590 Cov.: 32

Gnomad AFR AF: 0.0448

Gnomad AMI AF: 0.0760

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.156

Gnomad EAS AF: 0.187

Gnomad SAS AF: 0.0670

Gnomad FIN AF: 0.207

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.175

Gnomad OTH AF: 0.129

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

GnomAD4 genome AF: 0.131 AC: 19968 AN: 152084 Hom.: 1585 Cov.: 32 AF XY: 0.131 AC XY: 9745 AN XY: 74344

African (AFR) AF: 0.0449 AC: 1862 AN: 41486

American (AMR) AF: 0.117 AC: 1786 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.156 AC: 540 AN: 3472

East Asian (EAS) AF: 0.186 AC: 962 AN: 5170

South Asian (SAS) AF: 0.0662 AC: 319 AN: 4818

European-Finnish (FIN) AF: 0.207 AC: 2185 AN: 10564

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.175 AC: 11928 AN: 67992

Other (OTH) AF: 0.133 AC: 281 AN: 2110

Alfa AF: 0.166 Hom.: 954

Bravo AF: 0.121

Asia WGS AF: 0.111 AC: 386 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	7.3
DANN	Benign	0.71
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs12769316; hg19: chr10-104152751;