rs7988007

Variant names:

• chr13-58414137-A-C
• rs7988007

Your query was ambiguous. Multiple possible variants found:

• chr13-58414137-A-C
• chr13-58414137-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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;