chr12-9749903-G-T

Variant names:

• chr12-9749903-G-T
• rs929615

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 0.681 in 152,030 control chromosomes in the GnomAD database, including 37,311 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 0.68 (37311 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.830
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.928 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: 0.681 AC: 103447 AN: 151912 Hom.: 37308 Cov.: 32

Gnomad AFR AF: 0.417

Gnomad AMI AF: 0.657

Gnomad AMR AF: 0.744

Gnomad ASJ AF: 0.763

Gnomad EAS AF: 0.951

Gnomad SAS AF: 0.836

Gnomad FIN AF: 0.805

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.770

Gnomad OTH AF: 0.722

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

GnomAD4 genome AF: 0.681 AC: 103483 AN: 152030 Hom.: 37311 Cov.: 32 AF XY: 0.687 AC XY: 51079 AN XY: 74300

African (AFR) AF: 0.417 AC: 17253 AN: 41374

American (AMR) AF: 0.744 AC: 11381 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.763 AC: 2648 AN: 3472

East Asian (EAS) AF: 0.951 AC: 4932 AN: 5188

South Asian (SAS) AF: 0.836 AC: 4040 AN: 4830

European-Finnish (FIN) AF: 0.805 AC: 8512 AN: 10568

Middle Eastern (MID) AF: 0.810 AC: 238 AN: 294

European-Non Finnish (NFE) AF: 0.770 AC: 52355 AN: 67992

Other (OTH) AF: 0.724 AC: 1525 AN: 2106

Alfa AF: 0.708 Hom.: 5496

Bravo AF: 0.665

Asia WGS AF: 0.861 AC: 2996 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.4
DANN	Benign	0.31
PhyloP100		0.83

Splicing

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

Other links and lift over

dbSNP: rs929615; hg19: chr12-9902499;