13-107138053-C-G

Variant names:

• chr13-107138053-C-G
• rs35669975

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 0.379 in 151,998 control chromosomes in the GnomAD database, including 11,459 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 0.38 (11459 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.29
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.608 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: 0.379 AC: 57583 AN: 151880 Hom.: 11450 Cov.: 32

Gnomad AFR AF: 0.292

Gnomad AMI AF: 0.331

Gnomad AMR AF: 0.426

Gnomad ASJ AF: 0.344

Gnomad EAS AF: 0.626

Gnomad SAS AF: 0.544

Gnomad FIN AF: 0.443

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.385

Gnomad OTH AF: 0.356

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

GnomAD4 genome AF: 0.379 AC: 57613 AN: 151998 Hom.: 11459 Cov.: 32 AF XY: 0.387 AC XY: 28754 AN XY: 74302

African (AFR) AF: 0.291 AC: 12073 AN: 41464

American (AMR) AF: 0.426 AC: 6509 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.344 AC: 1193 AN: 3466

East Asian (EAS) AF: 0.626 AC: 3224 AN: 5154

South Asian (SAS) AF: 0.542 AC: 2611 AN: 4814

European-Finnish (FIN) AF: 0.443 AC: 4677 AN: 10558

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.385 AC: 26160 AN: 67956

Other (OTH) AF: 0.363 AC: 768 AN: 2114

Alfa AF: 0.237 Hom.: 559

Bravo AF: 0.374

Asia WGS AF: 0.541 AC: 1878 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.0040
DANN	Benign	0.32
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs35669975; hg19: chr13-107790401;