rs6494964

chr15-33201020-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_932090.3(LOC105370759):n.806+1638G>A variant causes a intron, non coding transcript 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: LOC105370759 XR_932090.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.50

Genes affected

LOC105370759 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC105370759	XR_932090.3	n.806+1638G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.542

Gnomad4 AMR AF: 0.306

Gnomad4 ASJ AF: 0.204

Gnomad4 EAS AF: 0.555

Gnomad4 SAS AF: 0.259

Gnomad4 FIN AF: 0.255

Gnomad4 NFE AF: 0.307

Gnomad4 OTH AF: 0.341

Alfa AF: 0.314 Hom.: 11307

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6494964; hg19: chr15-33493221;