chr14-98174878-G-A

Variant names:

• chr14-98174878-G-A
• rs7152530
• ENST00000555776.1:n.121+30145C>T

Variant summary

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

The ENST00000555776.1(ENSG00000259097):​n.121+30145C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.346 in 151,914 control chromosomes in the GnomAD database, including 9,425 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 0.35 (9425 hom., cov: 32)
• Consequence: ENSG00000259097 ENST00000555776.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.93
• Publications: 8 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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.392 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
ENSG00000259097	ENST00000555776.1	n.121+30145C>T		intron_variant	Intron 1 of 2	4
ENSG00000259097	ENST00000733052.1	n.121-11773C>T		intron_variant	Intron 1 of 1
ENSG00000259097	ENST00000733053.1	n.113-11770C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.346 AC: 52468 AN: 151798 Hom.: 9412 Cov.: 32

Gnomad AFR AF: 0.397

Gnomad AMI AF: 0.319

Gnomad AMR AF: 0.310

Gnomad ASJ AF: 0.347

Gnomad EAS AF: 0.193

Gnomad SAS AF: 0.265

Gnomad FIN AF: 0.235

Gnomad MID AF: 0.376

Gnomad NFE AF: 0.357

Gnomad OTH AF: 0.359

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

GnomAD4 genome AF: 0.346 AC: 52534 AN: 151914 Hom.: 9425 Cov.: 32 AF XY: 0.337 AC XY: 24989 AN XY: 74256

African (AFR) AF: 0.397 AC: 16418 AN: 41368

American (AMR) AF: 0.310 AC: 4728 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.347 AC: 1202 AN: 3468

East Asian (EAS) AF: 0.194 AC: 999 AN: 5158

South Asian (SAS) AF: 0.267 AC: 1281 AN: 4802

European-Finnish (FIN) AF: 0.235 AC: 2483 AN: 10572

Middle Eastern (MID) AF: 0.387 AC: 113 AN: 292

European-Non Finnish (NFE) AF: 0.357 AC: 24257 AN: 67962

Other (OTH) AF: 0.362 AC: 763 AN: 2108

Alfa AF: 0.354 Hom.: 16773

Bravo AF: 0.355

Asia WGS AF: 0.258 AC: 897 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	0.10
DANN	Benign	0.64
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs7152530; hg19: chr14-98641215;