rs6473464

Variant names:

• chr8-83683361-G-T
• rs6473464
• ENST00000732288.1:n.363+9789C>A

Variant summary

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

The ENST00000732288.1(ENSG00000295739):​n.363+9789C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.638 in 151,774 control chromosomes in the GnomAD database, including 32,618 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 0.64 (32618 hom., cov: 31)
• Consequence: ENSG00000295739 ENST00000732288.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.322
• Publications: 1 publications found

Genes affected

ENSG00000295739 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.859 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375932	XR_001745724.1	n.200+3089C>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000295739	ENST00000732288.1	n.363+9789C>A		intron_variant	Intron 1 of 2
ENSG00000295739	ENST00000732289.1	n.427+3089C>A		intron_variant	Intron 2 of 3
ENSG00000295739	ENST00000732290.1	n.427+3089C>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.638 AC: 96784 AN: 151656 Hom.: 32562 Cov.: 31

Gnomad AFR AF: 0.866

Gnomad AMI AF: 0.458

Gnomad AMR AF: 0.644

Gnomad ASJ AF: 0.455

Gnomad EAS AF: 0.677

Gnomad SAS AF: 0.514

Gnomad FIN AF: 0.490

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.541

Gnomad OTH AF: 0.603

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

GnomAD4 genome AF: 0.638 AC: 96897 AN: 151774 Hom.: 32618 Cov.: 31 AF XY: 0.634 AC XY: 47015 AN XY: 74204

African (AFR) AF: 0.866 AC: 35954 AN: 41510

American (AMR) AF: 0.644 AC: 9815 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.455 AC: 1578 AN: 3466

East Asian (EAS) AF: 0.676 AC: 3473 AN: 5134

South Asian (SAS) AF: 0.513 AC: 2469 AN: 4810

European-Finnish (FIN) AF: 0.490 AC: 5166 AN: 10538

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.540 AC: 36633 AN: 67784

Other (OTH) AF: 0.605 AC: 1271 AN: 2102

Alfa AF: 0.599 Hom.: 12181

Bravo AF: 0.662

Asia WGS AF: 0.667 AC: 2314 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	0.29
DANN	Benign	0.33
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs6473464; hg19: chr8-84595596;