12-49947827-T-C

Variant names:

• chr12-49947827-T-C
• rs7305534

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 0.393 in 151,934 control chromosomes in the GnomAD database, including 12,362 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 0.39 (12362 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.655
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.498 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: 0.393 AC: 59595 AN: 151816 Hom.: 12330 Cov.: 32

Gnomad AFR AF: 0.504

Gnomad AMI AF: 0.395

Gnomad AMR AF: 0.462

Gnomad ASJ AF: 0.412

Gnomad EAS AF: 0.464

Gnomad SAS AF: 0.516

Gnomad FIN AF: 0.288

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.311

Gnomad OTH AF: 0.388

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

GnomAD4 genome AF: 0.393 AC: 59670 AN: 151934 Hom.: 12362 Cov.: 32 AF XY: 0.394 AC XY: 29288 AN XY: 74272

African (AFR) AF: 0.504 AC: 20875 AN: 41424

American (AMR) AF: 0.462 AC: 7052 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.412 AC: 1429 AN: 3472

East Asian (EAS) AF: 0.464 AC: 2385 AN: 5136

South Asian (SAS) AF: 0.515 AC: 2480 AN: 4818

European-Finnish (FIN) AF: 0.288 AC: 3039 AN: 10562

Middle Eastern (MID) AF: 0.395 AC: 116 AN: 294

European-Non Finnish (NFE) AF: 0.311 AC: 21102 AN: 67938

Other (OTH) AF: 0.395 AC: 833 AN: 2110

Alfa AF: 0.348 Hom.: 18254

Bravo AF: 0.408

Asia WGS AF: 0.560 AC: 1947 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.067
DANN	Benign	0.30
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs7305534; hg19: chr12-50341610;