rs1442295

chr15-87419456-T-C

Variant summary

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

The ENST00000665121.1(ENSG00000259560):n.332+10442A>G 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 0.269 in 152,058 control chromosomes in the GnomAD database, including 6,314 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 0.27 (6314 hom., cov: 32)
• Consequence: ENST00000665121.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.845

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.594 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370956	XR_932585.3	n.626-185A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000665121.1	n.332+10442A>G		intron_variant, non_coding_transcript_variant
	ENST00000656130.1	n.176+13653A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.269 AC: 40874 AN: 151940 Hom.: 6300 Cov.: 32

Gnomad AFR AF: 0.347

Gnomad AMI AF: 0.137

Gnomad AMR AF: 0.316

Gnomad ASJ AF: 0.180

Gnomad EAS AF: 0.612

Gnomad SAS AF: 0.359

Gnomad FIN AF: 0.202

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.196

Gnomad OTH AF: 0.251

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

GnomAD4 genome AF: 0.269 AC: 40907 AN: 152058 Hom.: 6314 Cov.: 32 AF XY: 0.273 AC XY: 20279 AN XY: 74320

Gnomad4 AFR AF: 0.347

Gnomad4 AMR AF: 0.316

Gnomad4 ASJ AF: 0.180

Gnomad4 EAS AF: 0.612

Gnomad4 SAS AF: 0.359

Gnomad4 FIN AF: 0.202

Gnomad4 NFE AF: 0.196

Gnomad4 OTH AF: 0.255

Alfa AF: 0.241 Hom.: 1755

Bravo AF: 0.281

Asia WGS AF: 0.477 AC: 1659 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	1.9
Dann	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1442295; hg19: chr15-87962687;