12-38283606-T-C

Variant names:

• chr12-38283606-T-C
• rs1843910

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 0.491 in 151,808 control chromosomes in the GnomAD database, including 18,651 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 0.49 (18651 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0290
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.551 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: 0.491 AC: 74448 AN: 151690 Hom.: 18632 Cov.: 32

Gnomad AFR AF: 0.558

Gnomad AMI AF: 0.538

Gnomad AMR AF: 0.463

Gnomad ASJ AF: 0.548

Gnomad EAS AF: 0.286

Gnomad SAS AF: 0.401

Gnomad FIN AF: 0.400

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.488

Gnomad OTH AF: 0.522

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

GnomAD4 genome AF: 0.491 AC: 74512 AN: 151808 Hom.: 18651 Cov.: 32 AF XY: 0.484 AC XY: 35907 AN XY: 74164

African (AFR) AF: 0.557 AC: 23092 AN: 41422

American (AMR) AF: 0.463 AC: 7049 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.548 AC: 1898 AN: 3466

East Asian (EAS) AF: 0.285 AC: 1472 AN: 5162

South Asian (SAS) AF: 0.401 AC: 1929 AN: 4816

European-Finnish (FIN) AF: 0.400 AC: 4211 AN: 10538

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.488 AC: 33113 AN: 67852

Other (OTH) AF: 0.526 AC: 1112 AN: 2114

Alfa AF: 0.494 Hom.: 2448

Bravo AF: 0.498

Asia WGS AF: 0.372 AC: 1295 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	4.1
DANN	Benign	0.52
PhyloP100		-0.029

Splicing

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

Other links and lift over

dbSNP: rs1843910; hg19: chr12-38677408;