13-105407907-A-G

Variant names:

• chr13-105407907-A-G
• rs7329966

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 0.629 in 152,024 control chromosomes in the GnomAD database, including 31,348 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 0.63 (31348 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.241
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.796 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: 0.629 AC: 95492 AN: 151906 Hom.: 31291 Cov.: 33

Gnomad AFR AF: 0.803

Gnomad AMI AF: 0.419

Gnomad AMR AF: 0.664

Gnomad ASJ AF: 0.444

Gnomad EAS AF: 0.738

Gnomad SAS AF: 0.541

Gnomad FIN AF: 0.626

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.526

Gnomad OTH AF: 0.597

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

GnomAD4 genome AF: 0.629 AC: 95611 AN: 152024 Hom.: 31348 Cov.: 33 AF XY: 0.631 AC XY: 46890 AN XY: 74280

African (AFR) AF: 0.803 AC: 33325 AN: 41494

American (AMR) AF: 0.664 AC: 10141 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.444 AC: 1539 AN: 3468

East Asian (EAS) AF: 0.738 AC: 3820 AN: 5176

South Asian (SAS) AF: 0.541 AC: 2608 AN: 4818

European-Finnish (FIN) AF: 0.626 AC: 6590 AN: 10530

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.527 AC: 35781 AN: 67960

Other (OTH) AF: 0.597 AC: 1260 AN: 2110

Alfa AF: 0.569 Hom.: 58738

Bravo AF: 0.642

Asia WGS AF: 0.642 AC: 2228 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	7.9
DANN	Benign	0.78
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs7329966; hg19: chr13-106060256;