13-72298068-A-G

Variant names:

• chr13-72298068-A-G
• rs1146849

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 0.688 in 151,412 control chromosomes in the GnomAD database, including 36,416 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 0.69 (36416 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04
• Publications: 4 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 (EAS) allele frequency at 95% confidence interval = 0.835 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: 0.688 AC: 104070 AN: 151294 Hom.: 36396 Cov.: 32

Gnomad AFR AF: 0.574

Gnomad AMI AF: 0.843

Gnomad AMR AF: 0.639

Gnomad ASJ AF: 0.780

Gnomad EAS AF: 0.856

Gnomad SAS AF: 0.799

Gnomad FIN AF: 0.751

Gnomad MID AF: 0.772

Gnomad NFE AF: 0.730

Gnomad OTH AF: 0.714

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

GnomAD4 genome AF: 0.688 AC: 104137 AN: 151412 Hom.: 36416 Cov.: 32 AF XY: 0.690 AC XY: 51084 AN XY: 73984

African (AFR) AF: 0.574 AC: 23765 AN: 41388

American (AMR) AF: 0.639 AC: 9694 AN: 15176

Ashkenazi Jewish (ASJ) AF: 0.780 AC: 2703 AN: 3466

East Asian (EAS) AF: 0.856 AC: 4395 AN: 5134

South Asian (SAS) AF: 0.800 AC: 3867 AN: 4832

European-Finnish (FIN) AF: 0.751 AC: 7946 AN: 10578

Middle Eastern (MID) AF: 0.765 AC: 225 AN: 294

European-Non Finnish (NFE) AF: 0.730 AC: 49266 AN: 67528

Other (OTH) AF: 0.717 AC: 1509 AN: 2106

Alfa AF: 0.712 Hom.: 53695

Bravo AF: 0.675

Asia WGS AF: 0.831 AC: 2890 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.1
DANN	Benign	0.84
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs1146849; hg19: chr13-72872206;