13-106741883-T-C

Variant names:

• chr13-106741883-T-C
• rs1330948

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 0.221 in 152,178 control chromosomes in the GnomAD database, including 3,981 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 0.22 (3981 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.59
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.258 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: 0.221 AC: 33540 AN: 152060 Hom.: 3977 Cov.: 33

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.253

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.264

Gnomad EAS AF: 0.114

Gnomad SAS AF: 0.248

Gnomad FIN AF: 0.354

Gnomad MID AF: 0.140

Gnomad NFE AF: 0.261

Gnomad OTH AF: 0.203

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

GnomAD4 genome AF: 0.221 AC: 33569 AN: 152178 Hom.: 3981 Cov.: 33 AF XY: 0.223 AC XY: 16585 AN XY: 74396

African (AFR) AF: 0.143 AC: 5923 AN: 41532

American (AMR) AF: 0.180 AC: 2759 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.264 AC: 916 AN: 3470

East Asian (EAS) AF: 0.114 AC: 589 AN: 5182

South Asian (SAS) AF: 0.250 AC: 1206 AN: 4826

European-Finnish (FIN) AF: 0.354 AC: 3741 AN: 10578

Middle Eastern (MID) AF: 0.130 AC: 38 AN: 292

European-Non Finnish (NFE) AF: 0.261 AC: 17737 AN: 68000

Other (OTH) AF: 0.205 AC: 430 AN: 2102

Alfa AF: 0.255 Hom.: 2669

Bravo AF: 0.204

Asia WGS AF: 0.194 AC: 671 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.0080
DANN	Benign	0.49
PhyloP100		-3.6

Splicing

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

Other links and lift over

dbSNP: rs1330948; hg19: chr13-107394231;