chr12-74660813-A-G

Variant names:

• chr12-74660813-A-G
• rs7311660

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 0.467 in 151,978 control chromosomes in the GnomAD database, including 18,823 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 0.47 (18823 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.08
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.729 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: 0.467 AC: 70851 AN: 151860 Hom.: 18796 Cov.: 32

Gnomad AFR AF: 0.736

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.401

Gnomad ASJ AF: 0.303

Gnomad EAS AF: 0.357

Gnomad SAS AF: 0.439

Gnomad FIN AF: 0.364

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.357

Gnomad OTH AF: 0.436

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

GnomAD4 genome AF: 0.467 AC: 70924 AN: 151978 Hom.: 18823 Cov.: 32 AF XY: 0.465 AC XY: 34505 AN XY: 74264

African (AFR) AF: 0.736 AC: 30522 AN: 41470

American (AMR) AF: 0.401 AC: 6110 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.303 AC: 1052 AN: 3470

East Asian (EAS) AF: 0.358 AC: 1842 AN: 5148

South Asian (SAS) AF: 0.438 AC: 2114 AN: 4828

European-Finnish (FIN) AF: 0.364 AC: 3840 AN: 10552

Middle Eastern (MID) AF: 0.439 AC: 129 AN: 294

European-Non Finnish (NFE) AF: 0.357 AC: 24270 AN: 67940

Other (OTH) AF: 0.439 AC: 927 AN: 2112

Alfa AF: 0.391 Hom.: 5546

Bravo AF: 0.479

Asia WGS AF: 0.398 AC: 1386 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.017
DANN	Benign	0.47
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs7311660; hg19: chr12-75054593;