13-75202132-G-T

Variant names:

• chr13-75202132-G-T
• rs548097

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 0.926 in 152,264 control chromosomes in the GnomAD database, including 66,024 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 0.93 (66024 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.772
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.977 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: 0.927 AC: 140975 AN: 152146 Hom.: 65987 Cov.: 32

Gnomad AFR AF: 0.776

Gnomad AMI AF: 0.997

Gnomad AMR AF: 0.967

Gnomad ASJ AF: 0.995

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.997

Gnomad FIN AF: 0.993

Gnomad MID AF: 0.956

Gnomad NFE AF: 0.983

Gnomad OTH AF: 0.946

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

GnomAD4 genome AF: 0.926 AC: 141071 AN: 152264 Hom.: 66024 Cov.: 32 AF XY: 0.929 AC XY: 69147 AN XY: 74446

African (AFR) AF: 0.776 AC: 32195 AN: 41496

American (AMR) AF: 0.967 AC: 14797 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.995 AC: 3454 AN: 3472

East Asian (EAS) AF: 0.997 AC: 5173 AN: 5188

South Asian (SAS) AF: 0.997 AC: 4811 AN: 4824

European-Finnish (FIN) AF: 0.993 AC: 10546 AN: 10620

Middle Eastern (MID) AF: 0.952 AC: 280 AN: 294

European-Non Finnish (NFE) AF: 0.983 AC: 66917 AN: 68042

Other (OTH) AF: 0.943 AC: 1991 AN: 2112

Alfa AF: 0.966 Hom.: 232847

Bravo AF: 0.918

Asia WGS AF: 0.972 AC: 3382 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.38
DANN	Benign	0.24
PhyloP100		-0.77

Splicing

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

Other links and lift over

dbSNP: rs548097; hg19: chr13-75776268;