rs7152623

Variant names:

• chr14-98121984-G-A
• rs7152623
• ENST00000555776.1:n.122-41459C>T

Your query was ambiguous. Multiple possible variants found:

• chr14-98121984-G-A
• chr14-98121984-G-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000555776.1(ENSG00000259097):​n.122-41459C>T variant causes a intron 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: ENSG00000259097 ENST00000555776.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.95
• Publications: 21 publications found

Genes affected

ENSG00000259097 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC105370655	XR_001750876.2	n.96-41459C>T		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000259097	ENST00000555776.1	n.122-41459C>T		intron_variant	Intron 1 of 2	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

African (AFR) AF: 0.249 AC: 10305 AN: 41462

American (AMR) AF: 0.317 AC: 4852 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.372 AC: 1289 AN: 3468

East Asian (EAS) AF: 0.192 AC: 987 AN: 5154

South Asian (SAS) AF: 0.314 AC: 1515 AN: 4826

European-Finnish (FIN) AF: 0.365 AC: 3852 AN: 10548

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.393 AC: 26689 AN: 67982

Other (OTH) AF: 0.359 AC: 759 AN: 2116

Alfa AF: 0.365 Hom.: 15471

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
PhyloP100		-3.0

Splicing

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

Other links and lift over

dbSNP: rs7152623; hg19: chr14-98588321;