rs7152623

chr14-98121984-G-Achr14-98121984-G-C

Variant summary

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

The ENST00000555776.1(ENSG00000259097):n.122-41459C>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 0.333 in 152,042 control chromosomes in the GnomAD database, including 8,843 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 0.33 (8843 hom., cov: 32)
• Consequence: ENST00000555776.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.95

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 (NFE) allele frequency at 95% confidence interval = 0.389 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370655	XR_001750876.2	n.96-41459C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000555776.1	n.122-41459C>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.333 AC: 50649 AN: 151924 Hom.: 8841 Cov.: 32

Gnomad AFR AF: 0.248

Gnomad AMI AF: 0.358

Gnomad AMR AF: 0.318

Gnomad ASJ AF: 0.372

Gnomad EAS AF: 0.191

Gnomad SAS AF: 0.315

Gnomad FIN AF: 0.365

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.393

Gnomad OTH AF: 0.356

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

GnomAD4 genome AF: 0.333 AC: 50689 AN: 152042 Hom.: 8843 Cov.: 32 AF XY: 0.330 AC XY: 24554 AN XY: 74308

Gnomad4 AFR AF: 0.249

Gnomad4 AMR AF: 0.317

Gnomad4 ASJ AF: 0.372

Gnomad4 EAS AF: 0.192

Gnomad4 SAS AF: 0.314

Gnomad4 FIN AF: 0.365

Gnomad4 NFE AF: 0.393

Gnomad4 OTH AF: 0.359

Alfa AF: 0.382 Hom.: 9597

Bravo AF: 0.326

Asia WGS AF: 0.264 AC: 918 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	0.013
Dann	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7152623; hg19: chr14-98588321;