chr13-71930573-A-G

Variant names:

• chr13-71930573-A-G
• rs1460456

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 0.197 in 152,162 control chromosomes in the GnomAD database, including 3,672 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 0.20 (3672 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.347
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.532 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.197 AC: 29962 AN: 152044 Hom.: 3665 Cov.: 33

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.276

Gnomad AMR AF: 0.336

Gnomad ASJ AF: 0.243

Gnomad EAS AF: 0.549

Gnomad SAS AF: 0.284

Gnomad FIN AF: 0.246

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.144

Gnomad OTH AF: 0.210

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

GnomAD4 genome AF: 0.197 AC: 29988 AN: 152162 Hom.: 3672 Cov.: 33 AF XY: 0.209 AC XY: 15549 AN XY: 74368

African (AFR) AF: 0.160 AC: 6647 AN: 41528

American (AMR) AF: 0.336 AC: 5147 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.243 AC: 844 AN: 3470

East Asian (EAS) AF: 0.549 AC: 2833 AN: 5162

South Asian (SAS) AF: 0.285 AC: 1372 AN: 4814

European-Finnish (FIN) AF: 0.246 AC: 2600 AN: 10570

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.144 AC: 9794 AN: 68004

Other (OTH) AF: 0.209 AC: 441 AN: 2112

Alfa AF: 0.150 Hom.: 1598

Bravo AF: 0.205

Asia WGS AF: 0.375 AC: 1302 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.1
DANN	Benign	0.85
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs1460456; hg19: chr13-72504711;