13-72297506-T-C

Variant names:

• chr13-72297506-T-C
• rs1146848

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 0.632 in 151,450 control chromosomes in the GnomAD database, including 31,424 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 0.63 (31424 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.548
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.822 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: 0.632 AC: 95700 AN: 151330 Hom.: 31410 Cov.: 32

Gnomad AFR AF: 0.455

Gnomad AMI AF: 0.816

Gnomad AMR AF: 0.599

Gnomad ASJ AF: 0.746

Gnomad EAS AF: 0.844

Gnomad SAS AF: 0.782

Gnomad FIN AF: 0.753

Gnomad MID AF: 0.710

Gnomad NFE AF: 0.693

Gnomad OTH AF: 0.660

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

GnomAD4 genome AF: 0.632 AC: 95746 AN: 151450 Hom.: 31424 Cov.: 32 AF XY: 0.638 AC XY: 47194 AN XY: 73998

African (AFR) AF: 0.454 AC: 18782 AN: 41354

American (AMR) AF: 0.599 AC: 9103 AN: 15196

Ashkenazi Jewish (ASJ) AF: 0.746 AC: 2583 AN: 3462

East Asian (EAS) AF: 0.843 AC: 4325 AN: 5128

South Asian (SAS) AF: 0.784 AC: 3777 AN: 4818

European-Finnish (FIN) AF: 0.753 AC: 7969 AN: 10582

Middle Eastern (MID) AF: 0.702 AC: 205 AN: 292

European-Non Finnish (NFE) AF: 0.693 AC: 46860 AN: 67598

Other (OTH) AF: 0.663 AC: 1399 AN: 2110

Alfa AF: 0.642 Hom.: 10449

Bravo AF: 0.613

Asia WGS AF: 0.801 AC: 2777 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	9.6
DANN	Benign	0.84
PhyloP100		0.55

Splicing

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

Other links and lift over

dbSNP: rs1146848; hg19: chr13-72871644;