rs13233885

Variant names:

• chr7-54064308-T-C
• rs13233885

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 0.188 in 152,004 control chromosomes in the GnomAD database, including 3,119 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 0.19 (3119 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0650
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.233 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: 0.188 AC: 28494 AN: 151886 Hom.: 3115 Cov.: 32

Gnomad AFR AF: 0.0970

Gnomad AMI AF: 0.326

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.0589

Gnomad SAS AF: 0.211

Gnomad FIN AF: 0.302

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.236

Gnomad OTH AF: 0.158

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

GnomAD4 genome AF: 0.188 AC: 28519 AN: 152004 Hom.: 3119 Cov.: 32 AF XY: 0.192 AC XY: 14295 AN XY: 74298

African (AFR) AF: 0.0970 AC: 4025 AN: 41474

American (AMR) AF: 0.180 AC: 2739 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.149 AC: 516 AN: 3470

East Asian (EAS) AF: 0.0590 AC: 304 AN: 5152

South Asian (SAS) AF: 0.211 AC: 1019 AN: 4826

European-Finnish (FIN) AF: 0.302 AC: 3187 AN: 10550

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.236 AC: 16068 AN: 67958

Other (OTH) AF: 0.158 AC: 334 AN: 2112

Alfa AF: 0.199 Hom.: 568

Bravo AF: 0.173

Asia WGS AF: 0.129 AC: 450 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	4.1
DANN	Benign	0.54
PhyloP100		-0.065

Splicing

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

Other links and lift over

dbSNP: rs13233885; hg19: chr7-54132001;