rs7988007

chr13-58414137-A-Cchr13-58414137-A-T

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 0.152 in 151,030 control chromosomes in the GnomAD database, including 2,331 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 0.15 (2331 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.39

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.428 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: 0.152 AC: 22955 AN: 150912 Hom.: 2329 Cov.: 32

Gnomad AFR AF: 0.0492

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.168

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.443

Gnomad SAS AF: 0.321

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.176

Gnomad OTH AF: 0.158

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

GnomAD4 genome AF: 0.152 AC: 22960 AN: 151030 Hom.: 2331 Cov.: 32 AF XY: 0.156 AC XY: 11518 AN XY: 73816

Gnomad4 AFR AF: 0.0490

Gnomad4 AMR AF: 0.169

Gnomad4 ASJ AF: 0.163

Gnomad4 EAS AF: 0.443

Gnomad4 SAS AF: 0.321

Gnomad4 FIN AF: 0.159

Gnomad4 NFE AF: 0.176

Gnomad4 OTH AF: 0.161

Alfa AF: 0.167 Hom.: 1737

Bravo AF: 0.146

Asia WGS AF: 0.327 AC: 1138 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	12
Dann	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7988007; hg19: chr13-58988271;