6-48545299-A-G

Variant names:

• chr6-48545299-A-G
• rs9463425
• ENST00000730502.1:n.282+6018A>G

Variant summary

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

The ENST00000730502.1(ENSG00000295504):​n.282+6018A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.537 in 151,898 control chromosomes in the GnomAD database, including 22,897 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 0.54 (22897 hom., cov: 31)
• Consequence: ENSG00000295504 ENST00000730502.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.481
• Publications: 3 publications found

Genes affected

ENSG00000295504 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.864 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986602	XR_001744151.1	n.466+6018A>G		intron_variant	Intron 3 of 3
LOC107986602	XR_001744152.1	n.234+6018A>G		intron_variant	Intron 2 of 2
LOC107986602	XR_001744154.1	n.455+6018A>G		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000295504	ENST00000730502.1	n.282+6018A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.537 AC: 81554 AN: 151780 Hom.: 22870 Cov.: 31

Gnomad AFR AF: 0.614

Gnomad AMI AF: 0.312

Gnomad AMR AF: 0.628

Gnomad ASJ AF: 0.496

Gnomad EAS AF: 0.885

Gnomad SAS AF: 0.662

Gnomad FIN AF: 0.465

Gnomad MID AF: 0.564

Gnomad NFE AF: 0.452

Gnomad OTH AF: 0.520

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

GnomAD4 genome AF: 0.537 AC: 81630 AN: 151898 Hom.: 22897 Cov.: 31 AF XY: 0.542 AC XY: 40263 AN XY: 74252

African (AFR) AF: 0.614 AC: 25438 AN: 41412

American (AMR) AF: 0.629 AC: 9594 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.496 AC: 1720 AN: 3468

East Asian (EAS) AF: 0.885 AC: 4558 AN: 5148

South Asian (SAS) AF: 0.660 AC: 3184 AN: 4822

European-Finnish (FIN) AF: 0.465 AC: 4914 AN: 10574

Middle Eastern (MID) AF: 0.565 AC: 165 AN: 292

European-Non Finnish (NFE) AF: 0.452 AC: 30678 AN: 67906

Other (OTH) AF: 0.520 AC: 1095 AN: 2106

Alfa AF: 0.482 Hom.: 30543

Bravo AF: 0.552

Asia WGS AF: 0.710 AC: 2464 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.95
DANN	Benign	0.56
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs9463425; hg19: chr6-48513035;