13-105812808-C-T

Variant names:

• chr13-105812808-C-T
• rs1927571

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 0.103 in 152,106 control chromosomes in the GnomAD database, including 993 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 0.10 (993 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.351
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.195 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.103 AC: 15607 AN: 151988 Hom.: 983 Cov.: 33

Gnomad AFR AF: 0.0668

Gnomad AMI AF: 0.0351

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.151

Gnomad FIN AF: 0.0859

Gnomad MID AF: 0.162

Gnomad NFE AF: 0.0964

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.103 AC: 15647 AN: 152106 Hom.: 993 Cov.: 33 AF XY: 0.104 AC XY: 7729 AN XY: 74366

African (AFR) AF: 0.0671 AC: 2782 AN: 41478

American (AMR) AF: 0.201 AC: 3069 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.165 AC: 571 AN: 3470

East Asian (EAS) AF: 0.135 AC: 699 AN: 5164

South Asian (SAS) AF: 0.152 AC: 732 AN: 4822

European-Finnish (FIN) AF: 0.0859 AC: 910 AN: 10592

Middle Eastern (MID) AF: 0.168 AC: 49 AN: 292

European-Non Finnish (NFE) AF: 0.0964 AC: 6553 AN: 68000

Other (OTH) AF: 0.118 AC: 250 AN: 2114

Alfa AF: 0.0288 Hom.: 17

Bravo AF: 0.110

Asia WGS AF: 0.122 AC: 424 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.9
DANN	Benign	0.54
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs1927571; hg19: chr13-106465157;