12-71935326-T-C

Variant names:

• chr12-71935326-T-C
• rs4448731

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 0.401 in 151,978 control chromosomes in the GnomAD database, including 13,845 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 0.40 (13845 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.63
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.485 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.401 AC: 60866 AN: 151860 Hom.: 13842 Cov.: 31

Gnomad AFR AF: 0.174

Gnomad AMI AF: 0.498

Gnomad AMR AF: 0.484

Gnomad ASJ AF: 0.489

Gnomad EAS AF: 0.422

Gnomad SAS AF: 0.399

Gnomad FIN AF: 0.538

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.490

Gnomad OTH AF: 0.444

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

GnomAD4 genome AF: 0.401 AC: 60881 AN: 151978 Hom.: 13845 Cov.: 31 AF XY: 0.405 AC XY: 30115 AN XY: 74284

African (AFR) AF: 0.174 AC: 7210 AN: 41460

American (AMR) AF: 0.484 AC: 7391 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.489 AC: 1696 AN: 3470

East Asian (EAS) AF: 0.422 AC: 2175 AN: 5148

South Asian (SAS) AF: 0.401 AC: 1925 AN: 4806

European-Finnish (FIN) AF: 0.538 AC: 5682 AN: 10558

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.490 AC: 33274 AN: 67942

Other (OTH) AF: 0.441 AC: 933 AN: 2116

Alfa AF: 0.435 Hom.: 1900

Bravo AF: 0.388

Asia WGS AF: 0.394 AC: 1369 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.1
DANN	Benign	0.48
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs4448731; hg19: chr12-72329106;