rs7988007

Variant names:

• chr13-58414137-A-C
• rs7988007
• ENST00000784591.1:n.608-15894A>C

Your query was ambiguous. Multiple possible variants found:

• chr13-58414137-A-C
• chr13-58414137-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000784591.1(ENSG00000302133):​n.608-15894A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000302133 ENST00000784591.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.39
• Publications: 5 publications found

Genes affected

ENSG00000302133 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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
ENSG00000302133	ENST00000784591.1	n.608-15894A>C		intron_variant	Intron 2 of 3

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

African (AFR) AF: 0.0490 AC: 2029 AN: 41438

American (AMR) AF: 0.169 AC: 2542 AN: 15084

Ashkenazi Jewish (ASJ) AF: 0.163 AC: 562 AN: 3448

East Asian (EAS) AF: 0.443 AC: 2271 AN: 5124

South Asian (SAS) AF: 0.321 AC: 1545 AN: 4808

European-Finnish (FIN) AF: 0.159 AC: 1685 AN: 10572

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.176 AC: 11850 AN: 67260

Other (OTH) AF: 0.161 AC: 336 AN: 2092

Alfa AF: 0.165 Hom.: 1998

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
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs7988007; hg19: chr13-58988271;