rs9302365

Positions:

• chr15-93253049-C-A
• chr15-93253049-C-G
• chr15-93253049-C-T

Variant summary

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

The ENST00000667030.1(ENSG00000257060):​n.172-6124C>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 0.484 in 151,702 control chromosomes in the GnomAD database, including 18,265 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 0.48 (18265 hom., cov: 31)
• Consequence: ENST00000667030.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.544

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.674 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105370982	XR_007064770.1	n.1096-6124C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000667030.1	n.172-6124C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.484 AC: 73296 AN: 151584 Hom.: 18246 Cov.: 31

Gnomad AFR AF: 0.419

Gnomad AMI AF: 0.529

Gnomad AMR AF: 0.603

Gnomad ASJ AF: 0.467

Gnomad EAS AF: 0.693

Gnomad SAS AF: 0.622

Gnomad FIN AF: 0.444

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.476

Gnomad OTH AF: 0.506

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

GnomAD4 genome AF: 0.484 AC: 73365 AN: 151702 Hom.: 18265 Cov.: 31 AF XY: 0.492 AC XY: 36463 AN XY: 74138

Gnomad4 AFR AF: 0.419

Gnomad4 AMR AF: 0.602

Gnomad4 ASJ AF: 0.467

Gnomad4 EAS AF: 0.693

Gnomad4 SAS AF: 0.621

Gnomad4 FIN AF: 0.444

Gnomad4 NFE AF: 0.476

Gnomad4 OTH AF: 0.510

Alfa AF: 0.494 Hom.: 25719

Bravo AF: 0.491

Asia WGS AF: 0.658 AC: 2287 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.9
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9302365; hg19: chr15-93796278;