rs7164923

chr15-23817768-C-T

Variant summary

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

The ENST00000658937.1(ENSG00000286973):n.460-6956C>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 0.064 in 152,206 control chromosomes in the GnomAD database, including 343 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 0.064 (343 hom., cov: 32)
• Consequence: ENST00000658937.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.459

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.109 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
	ENST00000658937.1	n.460-6956C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0639 AC: 9719 AN: 152088 Hom.: 339 Cov.: 32

Gnomad AFR AF: 0.0798

Gnomad AMI AF: 0.0395

Gnomad AMR AF: 0.0502

Gnomad ASJ AF: 0.0992

Gnomad EAS AF: 0.116

Gnomad SAS AF: 0.0503

Gnomad FIN AF: 0.0352

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0573

Gnomad OTH AF: 0.0602

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

GnomAD4 genome AF: 0.0640 AC: 9745 AN: 152206 Hom.: 343 Cov.: 32 AF XY: 0.0639 AC XY: 4758 AN XY: 74424

Gnomad4 AFR AF: 0.0801

Gnomad4 AMR AF: 0.0501

Gnomad4 ASJ AF: 0.0992

Gnomad4 EAS AF: 0.116

Gnomad4 SAS AF: 0.0506

Gnomad4 FIN AF: 0.0352

Gnomad4 NFE AF: 0.0573

Gnomad4 OTH AF: 0.0634

Alfa AF: 0.0598 Hom.: 27

Bravo AF: 0.0647

Asia WGS AF: 0.104 AC: 359 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	2.4
Dann	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7164923; hg19: chr15-24062915;