chr13-107121200-A-G

Variant names:

• chr13-107121200-A-G
• rs7329003

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 0.267 in 152,122 control chromosomes in the GnomAD database, including 5,703 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 0.27 (5703 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.70
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.385 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: 0.267 AC: 40612 AN: 152004 Hom.: 5708 Cov.: 33

Gnomad AFR AF: 0.332

Gnomad AMI AF: 0.0965

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.256

Gnomad EAS AF: 0.401

Gnomad SAS AF: 0.333

Gnomad FIN AF: 0.299

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.227

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.267 AC: 40625 AN: 152122 Hom.: 5703 Cov.: 33 AF XY: 0.271 AC XY: 20131 AN XY: 74366

African (AFR) AF: 0.332 AC: 13766 AN: 41484

American (AMR) AF: 0.200 AC: 3066 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.256 AC: 887 AN: 3466

East Asian (EAS) AF: 0.399 AC: 2062 AN: 5164

South Asian (SAS) AF: 0.332 AC: 1605 AN: 4828

European-Finnish (FIN) AF: 0.299 AC: 3161 AN: 10570

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

European-Non Finnish (NFE) AF: 0.227 AC: 15439 AN: 67992

Other (OTH) AF: 0.233 AC: 493 AN: 2112

Alfa AF: 0.251 Hom.: 815

Bravo AF: 0.260

Asia WGS AF: 0.368 AC: 1279 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.0010
DANN	Benign	0.27
PhyloP100		-5.7
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs7329003; hg19: chr13-107773548; COSMIC: COSV68600181;