13-72194571-T-G

Variant names:

• chr13-72194571-T-G
• rs4083578

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 0.654 in 152,030 control chromosomes in the GnomAD database, including 35,332 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 0.65 (35332 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.122
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.49).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.803 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: 0.654 AC: 99318 AN: 151912 Hom.: 35319 Cov.: 32

Gnomad AFR AF: 0.396

Gnomad AMI AF: 0.851

Gnomad AMR AF: 0.629

Gnomad ASJ AF: 0.817

Gnomad EAS AF: 0.289

Gnomad SAS AF: 0.739

Gnomad FIN AF: 0.765

Gnomad MID AF: 0.688

Gnomad NFE AF: 0.809

Gnomad OTH AF: 0.675

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

GnomAD4 genome AF: 0.654 AC: 99358 AN: 152030 Hom.: 35332 Cov.: 32 AF XY: 0.648 AC XY: 48166 AN XY: 74292

African (AFR) AF: 0.396 AC: 16398 AN: 41448

American (AMR) AF: 0.628 AC: 9583 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.817 AC: 2832 AN: 3466

East Asian (EAS) AF: 0.290 AC: 1501 AN: 5180

South Asian (SAS) AF: 0.739 AC: 3561 AN: 4816

European-Finnish (FIN) AF: 0.765 AC: 8082 AN: 10570

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

European-Non Finnish (NFE) AF: 0.809 AC: 54993 AN: 67972

Other (OTH) AF: 0.677 AC: 1429 AN: 2112

Alfa AF: 0.752 Hom.: 96775

Bravo AF: 0.627

Asia WGS AF: 0.557 AC: 1934 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.49
CADD	Benign	18
DANN	Benign	0.76
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs4083578; hg19: chr13-72768709;