rs7745887

Variant names:

• chr6-384546-G-C
• rs7745887
• ENST00000793853.1:n.394+2435C>G

Variant summary

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

The ENST00000793853.1(ENSG00000303358):​n.394+2435C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 152,160 control chromosomes in the GnomAD database, including 2,152 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 0.10 (2152 hom., cov: 32)
• Consequence: ENSG00000303358 ENST00000793853.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.547
• Publications: 3 publications found

Genes affected

ENSG00000303358 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.31 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
ENSG00000303358	ENST00000793853.1	n.394+2435C>G		intron_variant	Intron 1 of 1
ENSG00000303358	ENST00000793854.1	n.263+2435C>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.103 AC: 15675 AN: 152042 Hom.: 2136 Cov.: 32

Gnomad AFR AF: 0.314

Gnomad AMI AF: 0.0417

Gnomad AMR AF: 0.0572

Gnomad ASJ AF: 0.0199

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0143

Gnomad FIN AF: 0.00895

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0194

Gnomad OTH AF: 0.0963

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

GnomAD4 genome AF: 0.103 AC: 15731 AN: 152160 Hom.: 2152 Cov.: 32 AF XY: 0.101 AC XY: 7524 AN XY: 74418

African (AFR) AF: 0.315 AC: 13043 AN: 41440

American (AMR) AF: 0.0572 AC: 874 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0199 AC: 69 AN: 3472

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5182

South Asian (SAS) AF: 0.0141 AC: 68 AN: 4830

European-Finnish (FIN) AF: 0.00895 AC: 95 AN: 10614

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0194 AC: 1322 AN: 68014

Other (OTH) AF: 0.0953 AC: 201 AN: 2110

Alfa AF: 0.0695 Hom.: 177

Bravo AF: 0.117

Asia WGS AF: 0.0280 AC: 99 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.0
DANN	Benign	0.61
PhyloP100		0.55

Splicing

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

Other links and lift over

dbSNP: rs7745887; hg19: chr6-384546;