rs4075355

Variant names:

• chr14-104659175-G-A
• rs4075355
• ENST00000812077.1:n.160-5404C>T

Your query was ambiguous. Multiple possible variants found:

• chr14-104659175-G-A
• chr14-104659175-G-C
• chr14-104659175-G-T

Variant summary

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

The ENST00000812077.1(ENSG00000258736):​n.160-5404C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.203 in 152,092 control chromosomes in the GnomAD database, including 3,697 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 0.20 (3697 hom., cov: 32)
• Consequence: ENSG00000258736 ENST00000812077.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.194
• Publications: 3 publications found

Genes affected

ENSG00000258736 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.262 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
ENSG00000258736	ENST00000812077.1	n.160-5404C>T		intron_variant	Intron 1 of 1
ENSG00000258736	ENST00000812078.1	n.442-5404C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.203 AC: 30924 AN: 151974 Hom.: 3694 Cov.: 32

Gnomad AFR AF: 0.0874

Gnomad AMI AF: 0.203

Gnomad AMR AF: 0.252

Gnomad ASJ AF: 0.272

Gnomad EAS AF: 0.0491

Gnomad SAS AF: 0.209

Gnomad FIN AF: 0.230

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.266

Gnomad OTH AF: 0.243

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

GnomAD4 genome AF: 0.203 AC: 30930 AN: 152092 Hom.: 3697 Cov.: 32 AF XY: 0.202 AC XY: 15050 AN XY: 74338

African (AFR) AF: 0.0872 AC: 3621 AN: 41526

American (AMR) AF: 0.252 AC: 3845 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.272 AC: 945 AN: 3470

East Asian (EAS) AF: 0.0491 AC: 253 AN: 5156

South Asian (SAS) AF: 0.211 AC: 1014 AN: 4808

European-Finnish (FIN) AF: 0.230 AC: 2435 AN: 10596

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.266 AC: 18053 AN: 67942

Other (OTH) AF: 0.243 AC: 513 AN: 2114

Alfa AF: 0.112 Hom.: 193

Bravo AF: 0.199

Asia WGS AF: 0.139 AC: 482 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.8
DANN	Benign	0.81
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs4075355; hg19: chr14-105125512;