rs288742

Variant names:

• chr13-106849456-T-C
• rs288742

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 0.374 in 152,156 control chromosomes in the GnomAD database, including 12,303 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 0.37 (12303 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.472 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: 0.374 AC: 56825 AN: 152038 Hom.: 12301 Cov.: 33

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.562

Gnomad AMR AF: 0.452

Gnomad ASJ AF: 0.479

Gnomad EAS AF: 0.310

Gnomad SAS AF: 0.479

Gnomad FIN AF: 0.427

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.476

Gnomad OTH AF: 0.387

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

GnomAD4 genome AF: 0.374 AC: 56847 AN: 152156 Hom.: 12303 Cov.: 33 AF XY: 0.374 AC XY: 27841 AN XY: 74376

African (AFR) AF: 0.145 AC: 6029 AN: 41536

American (AMR) AF: 0.452 AC: 6901 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.479 AC: 1663 AN: 3470

East Asian (EAS) AF: 0.311 AC: 1606 AN: 5168

South Asian (SAS) AF: 0.478 AC: 2311 AN: 4830

European-Finnish (FIN) AF: 0.427 AC: 4518 AN: 10570

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.476 AC: 32386 AN: 67988

Other (OTH) AF: 0.388 AC: 820 AN: 2112

Alfa AF: 0.417 Hom.: 2119

Bravo AF: 0.364

Asia WGS AF: 0.386 AC: 1339 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	7.8
DANN	Benign	0.77
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs288742; hg19: chr13-107501804;