12-42772656-A-T

Variant names:

• chr12-42772656-A-T
• rs2138861

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 0.428 in 151,986 control chromosomes in the GnomAD database, including 14,810 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 0.43 (14810 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.487
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.812 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: 0.428 AC: 64935 AN: 151870 Hom.: 14776 Cov.: 32

Gnomad AFR AF: 0.465

Gnomad AMI AF: 0.509

Gnomad AMR AF: 0.523

Gnomad ASJ AF: 0.356

Gnomad EAS AF: 0.833

Gnomad SAS AF: 0.573

Gnomad FIN AF: 0.469

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.339

Gnomad OTH AF: 0.411

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

GnomAD4 genome AF: 0.428 AC: 65028 AN: 151986 Hom.: 14810 Cov.: 32 AF XY: 0.441 AC XY: 32756 AN XY: 74256

African (AFR) AF: 0.466 AC: 19311 AN: 41458

American (AMR) AF: 0.524 AC: 7998 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.356 AC: 1234 AN: 3468

East Asian (EAS) AF: 0.833 AC: 4306 AN: 5168

South Asian (SAS) AF: 0.573 AC: 2757 AN: 4814

European-Finnish (FIN) AF: 0.469 AC: 4940 AN: 10526

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.339 AC: 23040 AN: 67964

Other (OTH) AF: 0.417 AC: 880 AN: 2110

Alfa AF: 0.397 Hom.: 1363

Bravo AF: 0.434

Asia WGS AF: 0.712 AC: 2471 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.77
DANN	Benign	0.64
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs2138861; hg19: chr12-43166458;