chr12-65996188-T-C

Variant names:

• chr12-65996188-T-C
• rs10400419

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 0.548 in 152,064 control chromosomes in the GnomAD database, including 23,455 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 0.55 (23455 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.582
• Publications: 19 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 (EAS) allele frequency at 95% confidence interval = 0.84 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: 0.548 AC: 83319 AN: 151948 Hom.: 23430 Cov.: 33

Gnomad AFR AF: 0.484

Gnomad AMI AF: 0.587

Gnomad AMR AF: 0.623

Gnomad ASJ AF: 0.660

Gnomad EAS AF: 0.861

Gnomad SAS AF: 0.703

Gnomad FIN AF: 0.473

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.540

Gnomad OTH AF: 0.583

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

GnomAD4 genome AF: 0.548 AC: 83379 AN: 152064 Hom.: 23455 Cov.: 33 AF XY: 0.551 AC XY: 40968 AN XY: 74316

African (AFR) AF: 0.485 AC: 20111 AN: 41490

American (AMR) AF: 0.622 AC: 9508 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.660 AC: 2287 AN: 3466

East Asian (EAS) AF: 0.862 AC: 4458 AN: 5174

South Asian (SAS) AF: 0.703 AC: 3389 AN: 4818

European-Finnish (FIN) AF: 0.473 AC: 4995 AN: 10550

Middle Eastern (MID) AF: 0.646 AC: 190 AN: 294

European-Non Finnish (NFE) AF: 0.540 AC: 36685 AN: 67978

Other (OTH) AF: 0.579 AC: 1222 AN: 2110

Alfa AF: 0.561 Hom.: 41779

Bravo AF: 0.561

Asia WGS AF: 0.728 AC: 2532 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	0.18
DANN	Benign	0.38
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs10400419; hg19: chr12-66389968;