chr12-101219710-G-A

Variant names:

• chr12-101219710-G-A
• rs2712623

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 0.617 in 152,034 control chromosomes in the GnomAD database, including 30,006 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 0.62 (30006 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.127
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.784 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: 0.617 AC: 93724 AN: 151916 Hom.: 29957 Cov.: 32

Gnomad AFR AF: 0.791

Gnomad AMI AF: 0.532

Gnomad AMR AF: 0.565

Gnomad ASJ AF: 0.595

Gnomad EAS AF: 0.427

Gnomad SAS AF: 0.644

Gnomad FIN AF: 0.505

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.555

Gnomad OTH AF: 0.613

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

GnomAD4 genome AF: 0.617 AC: 93830 AN: 152034 Hom.: 30006 Cov.: 32 AF XY: 0.613 AC XY: 45550 AN XY: 74306

African (AFR) AF: 0.791 AC: 32828 AN: 41492

American (AMR) AF: 0.564 AC: 8608 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.595 AC: 2064 AN: 3468

East Asian (EAS) AF: 0.428 AC: 2214 AN: 5174

South Asian (SAS) AF: 0.644 AC: 3105 AN: 4818

European-Finnish (FIN) AF: 0.505 AC: 5319 AN: 10524

Middle Eastern (MID) AF: 0.592 AC: 173 AN: 292

European-Non Finnish (NFE) AF: 0.555 AC: 37735 AN: 67986

Other (OTH) AF: 0.615 AC: 1301 AN: 2114

Alfa AF: 0.575 Hom.: 95063

Bravo AF: 0.627

Asia WGS AF: 0.589 AC: 2046 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.85
DANN	Benign	0.62
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs2712623; hg19: chr12-101613488; COSMIC: COSV69617556;