rs6496932

chr15-85282336-C-Achr15-85282336-C-G

Variant summary

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

The ENST00000559518.1(ENSG00000291212):n.152-8168G>T 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 0.286 in 151,848 control chromosomes in the GnomAD database, including 7,141 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 0.29 (7141 hom., cov: 31)
• Consequence: ENST00000559518.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.484

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.437 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000559518.1	n.152-8168G>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.286 AC: 43379 AN: 151730 Hom.: 7121 Cov.: 31

Gnomad AFR AF: 0.442

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.253

Gnomad ASJ AF: 0.302

Gnomad EAS AF: 0.331

Gnomad SAS AF: 0.370

Gnomad FIN AF: 0.291

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.190

Gnomad OTH AF: 0.274

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

GnomAD4 genome AF: 0.286 AC: 43455 AN: 151848 Hom.: 7141 Cov.: 31 AF XY: 0.293 AC XY: 21771 AN XY: 74216

Gnomad4 AFR AF: 0.443

Gnomad4 AMR AF: 0.253

Gnomad4 ASJ AF: 0.302

Gnomad4 EAS AF: 0.331

Gnomad4 SAS AF: 0.371

Gnomad4 FIN AF: 0.291

Gnomad4 NFE AF: 0.190

Gnomad4 OTH AF: 0.277

Alfa AF: 0.213 Hom.: 8851

Bravo AF: 0.286

Asia WGS AF: 0.350 AC: 1217 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.55
Dann	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6496932; hg19: chr15-85825567;