chr13-57307948-C-T

Variant names:

• chr13-57307948-C-T
• rs10507612

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 0.0392 in 151,768 control chromosomes in the GnomAD database, including 340 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 0.039 (340 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.30
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.16 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: 0.0392 AC: 5939 AN: 151650 Hom.: 339 Cov.: 33

Gnomad AFR AF: 0.00889

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.00893

Gnomad EAS AF: 0.00231

Gnomad SAS AF: 0.0447

Gnomad FIN AF: 0.0310

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0336

Gnomad OTH AF: 0.0356

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

GnomAD4 genome AF: 0.0392 AC: 5944 AN: 151768 Hom.: 340 Cov.: 33 AF XY: 0.0413 AC XY: 3068 AN XY: 74206

African (AFR) AF: 0.00886 AC: 365 AN: 41202

American (AMR) AF: 0.165 AC: 2523 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.00893 AC: 31 AN: 3470

East Asian (EAS) AF: 0.00231 AC: 12 AN: 5186

South Asian (SAS) AF: 0.0442 AC: 213 AN: 4824

European-Finnish (FIN) AF: 0.0310 AC: 327 AN: 10546

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0336 AC: 2285 AN: 67980

Other (OTH) AF: 0.0352 AC: 74 AN: 2100

Alfa AF: 0.0363 Hom.: 32

Bravo AF: 0.0473

Asia WGS AF: 0.0250 AC: 85 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.29
DANN	Benign	0.28
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs10507612; hg19: chr13-57882082;