rs13235686

Positions:

• chr7-54059862-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.166 in 152,140 control chromosomes in the GnomAD database, including 2,427 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 0.17 (2427 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.513

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.202 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.166 AC: 25185 AN: 152022 Hom.: 2422 Cov.: 32

Gnomad AFR AF: 0.0912

Gnomad AMI AF: 0.322

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.135

Gnomad EAS AF: 0.0575

Gnomad SAS AF: 0.157

Gnomad FIN AF: 0.268

Gnomad MID AF: 0.0860

Gnomad NFE AF: 0.205

Gnomad OTH AF: 0.134

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

GnomAD4 genome AF: 0.166 AC: 25211 AN: 152140 Hom.: 2427 Cov.: 32 AF XY: 0.170 AC XY: 12655 AN XY: 74378

Gnomad4 AFR AF: 0.0913

Gnomad4 AMR AF: 0.166

Gnomad4 ASJ AF: 0.135

Gnomad4 EAS AF: 0.0576

Gnomad4 SAS AF: 0.158

Gnomad4 FIN AF: 0.268

Gnomad4 NFE AF: 0.205

Gnomad4 OTH AF: 0.135

Alfa AF: 0.189 Hom.: 3380

Bravo AF: 0.154

Asia WGS AF: 0.110 AC: 385 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.56
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13235686; hg19: chr7-54127555;