rs6494964

Variant names:

• chr15-33201020-G-A
• rs6494964
• ENST00000796872.1:n.290-3162G>A

Variant summary

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

The ENST00000796872.1(ENSG00000289896):​n.290-3162G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.371 in 151,946 control chromosomes in the GnomAD database, including 11,659 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 0.37 (11659 hom., cov: 32)
• Consequence: ENSG00000289896 ENST00000796872.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.50
• Publications: 6 publications found

Genes affected

ENSG00000289896 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.538 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370759	XR_932090.3	n.806+1638G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289896	ENST00000796872.1	n.290-3162G>A		intron_variant	Intron 1 of 2
ENSG00000289896	ENST00000796873.1	n.806+1638G>A		intron_variant	Intron 2 of 2
ENSG00000289896	ENST00000796874.1	n.600-3162G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.371 AC: 56340 AN: 151828 Hom.: 11647 Cov.: 32

Gnomad AFR AF: 0.542

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.306

Gnomad ASJ AF: 0.204

Gnomad EAS AF: 0.554

Gnomad SAS AF: 0.259

Gnomad FIN AF: 0.255

Gnomad MID AF: 0.239

Gnomad NFE AF: 0.307

Gnomad OTH AF: 0.341

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

GnomAD4 genome AF: 0.371 AC: 56398 AN: 151946 Hom.: 11659 Cov.: 32 AF XY: 0.366 AC XY: 27202 AN XY: 74260

African (AFR) AF: 0.542 AC: 22427 AN: 41414

American (AMR) AF: 0.306 AC: 4671 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.204 AC: 707 AN: 3470

East Asian (EAS) AF: 0.555 AC: 2859 AN: 5154

South Asian (SAS) AF: 0.259 AC: 1247 AN: 4808

European-Finnish (FIN) AF: 0.255 AC: 2691 AN: 10550

Middle Eastern (MID) AF: 0.257 AC: 75 AN: 292

European-Non Finnish (NFE) AF: 0.307 AC: 20883 AN: 67968

Other (OTH) AF: 0.341 AC: 721 AN: 2116

Alfa AF: 0.334 Hom.: 22838

Bravo AF: 0.385

Asia WGS AF: 0.419 AC: 1460 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.1
DANN	Benign	0.52
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs6494964; hg19: chr15-33493221;