rs7164923

Variant names:

• chr15-23817768-C-T
• rs7164923
• ENST00000658937.1:n.460-6956C>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 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: ENSG00000286973 ENST00000658937.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.459

Genes affected

ENSG00000286973 (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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286973	ENST00000658937.1	n.460-6956C>T		intron_variant	Intron 1 of 2

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;