rs10743288

Variant names:

• chr12-18906020-G-A
• rs10743288

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 0.737 in 152,044 control chromosomes in the GnomAD database, including 43,713 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 0.74 (43713 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0110
• Publications: 2 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 (EAS) allele frequency at 95% confidence interval = 0.856 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: 0.737 AC: 112019 AN: 151928 Hom.: 43688 Cov.: 31

Gnomad AFR AF: 0.451

Gnomad AMI AF: 0.829

Gnomad AMR AF: 0.839

Gnomad ASJ AF: 0.780

Gnomad EAS AF: 0.877

Gnomad SAS AF: 0.805

Gnomad FIN AF: 0.839

Gnomad MID AF: 0.706

Gnomad NFE AF: 0.853

Gnomad OTH AF: 0.757

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

GnomAD4 genome AF: 0.737 AC: 112070 AN: 152044 Hom.: 43713 Cov.: 31 AF XY: 0.738 AC XY: 54841 AN XY: 74334

African (AFR) AF: 0.451 AC: 18674 AN: 41414

American (AMR) AF: 0.839 AC: 12824 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.780 AC: 2706 AN: 3468

East Asian (EAS) AF: 0.878 AC: 4531 AN: 5162

South Asian (SAS) AF: 0.805 AC: 3874 AN: 4810

European-Finnish (FIN) AF: 0.839 AC: 8896 AN: 10600

Middle Eastern (MID) AF: 0.701 AC: 206 AN: 294

European-Non Finnish (NFE) AF: 0.853 AC: 57999 AN: 67994

Other (OTH) AF: 0.759 AC: 1604 AN: 2112

Alfa AF: 0.818 Hom.: 196970

Bravo AF: 0.727

Asia WGS AF: 0.842 AC: 2928 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	2.0
DANN	Benign	0.74
PhyloP100		-0.011

Splicing

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

Other links and lift over

dbSNP: rs10743288; hg19: chr12-19058954;