chr12-71927834-A-G

Variant names:

• chr12-71927834-A-G
• rs10506643

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 0.0912 in 152,188 control chromosomes in the GnomAD database, including 702 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 0.091 (702 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.66
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.135 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: 0.0912 AC: 13871 AN: 152070 Hom.: 700 Cov.: 32

Gnomad AFR AF: 0.0977

Gnomad AMI AF: 0.0724

Gnomad AMR AF: 0.0702

Gnomad ASJ AF: 0.0960

Gnomad EAS AF: 0.0214

Gnomad SAS AF: 0.144

Gnomad FIN AF: 0.0765

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0959

Gnomad OTH AF: 0.0919

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

GnomAD4 genome AF: 0.0912 AC: 13885 AN: 152188 Hom.: 702 Cov.: 32 AF XY: 0.0917 AC XY: 6828 AN XY: 74430

African (AFR) AF: 0.0977 AC: 4056 AN: 41514

American (AMR) AF: 0.0701 AC: 1071 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0960 AC: 333 AN: 3470

East Asian (EAS) AF: 0.0214 AC: 111 AN: 5184

South Asian (SAS) AF: 0.144 AC: 694 AN: 4820

European-Finnish (FIN) AF: 0.0765 AC: 811 AN: 10600

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0959 AC: 6518 AN: 67998

Other (OTH) AF: 0.0956 AC: 202 AN: 2112

Alfa AF: 0.104 Hom.: 113

Bravo AF: 0.0872

Asia WGS AF: 0.0980 AC: 342 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	9.4
DANN	Benign	0.46
PhyloP100		2.7

Splicing

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

Other links and lift over

dbSNP: rs10506643; hg19: chr12-72321614;