rs7386474

Variant names:

• chr8-141349451-A-G
• rs7386474
• ENST00000788345.1:n.115+2613A>G

Variant summary

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

The ENST00000788345.1(ENSG00000302644):​n.115+2613A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.412 in 151,448 control chromosomes in the GnomAD database, including 13,631 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 0.41 (13631 hom., cov: 30)
• Consequence: ENSG00000302644 ENST00000788345.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.982
• Publications: 14 publications found

Genes affected

ENSG00000302644 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.519 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
ENSG00000302644	ENST00000788345.1	n.115+2613A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.412 AC: 62378 AN: 151330 Hom.: 13612 Cov.: 30

Gnomad AFR AF: 0.288

Gnomad AMI AF: 0.469

Gnomad AMR AF: 0.471

Gnomad ASJ AF: 0.379

Gnomad EAS AF: 0.183

Gnomad SAS AF: 0.533

Gnomad FIN AF: 0.478

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.475

Gnomad OTH AF: 0.398

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

GnomAD4 genome AF: 0.412 AC: 62449 AN: 151448 Hom.: 13631 Cov.: 30 AF XY: 0.412 AC XY: 30474 AN XY: 73958

African (AFR) AF: 0.288 AC: 11854 AN: 41210

American (AMR) AF: 0.471 AC: 7177 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.379 AC: 1310 AN: 3458

East Asian (EAS) AF: 0.184 AC: 945 AN: 5124

South Asian (SAS) AF: 0.536 AC: 2568 AN: 4790

European-Finnish (FIN) AF: 0.478 AC: 5009 AN: 10472

Middle Eastern (MID) AF: 0.384 AC: 113 AN: 294

European-Non Finnish (NFE) AF: 0.475 AC: 32210 AN: 67870

Other (OTH) AF: 0.401 AC: 838 AN: 2092

Alfa AF: 0.446 Hom.: 36782

Bravo AF: 0.403

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	6.7
DANN	Benign	0.81
PhyloP100		0.98

Splicing

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

Other links and lift over

dbSNP: rs7386474; hg19: chr8-142359550;