7-54059862-T-C

Variant names:

• chr7-54059862-T-C
• rs13235686

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 0.166 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
• 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 (NFE) allele frequency at 95% confidence interval = 0.202 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: 0.166 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

African (AFR) AF: 0.0913 AC: 3792 AN: 41536

American (AMR) AF: 0.166 AC: 2532 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.135 AC: 467 AN: 3466

East Asian (EAS) AF: 0.0576 AC: 298 AN: 5170

South Asian (SAS) AF: 0.158 AC: 761 AN: 4830

European-Finnish (FIN) AF: 0.268 AC: 2840 AN: 10582

Middle Eastern (MID) AF: 0.0890 AC: 26 AN: 292

European-Non Finnish (NFE) AF: 0.205 AC: 13916 AN: 67978

Other (OTH) AF: 0.135 AC: 285 AN: 2112

Alfa AF: 0.186 Hom.: 8206

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
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs13235686; hg19: chr7-54127555;