rs4379175

Variant names:

• chr5-159377920-G-T
• rs4379175
• ENST00000635333.1:n.283-14613G>T

Variant summary

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

The ENST00000635333.1(ENSG00000249738):​n.283-14613G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.357 in 151,948 control chromosomes in the GnomAD database, including 9,848 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 0.36 (9848 hom., cov: 32)
• Consequence: ENSG00000249738 ENST00000635333.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.146
• Publications: 18 publications found

Genes affected

ENSG00000249738 (HGNC:58156):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.422 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
ENSG00000249738	ENST00000635333.1	n.283-14613G>T		intron_variant	Intron 3 of 7	5
ENSG00000249738	ENST00000641150.1	n.532+23799G>T		intron_variant	Intron 4 of 4
ENSG00000249738	ENST00000648969.1	n.53+23799G>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.357 AC: 54173 AN: 151830 Hom.: 9836 Cov.: 32

Gnomad AFR AF: 0.408

Gnomad AMI AF: 0.303

Gnomad AMR AF: 0.357

Gnomad ASJ AF: 0.287

Gnomad EAS AF: 0.437

Gnomad SAS AF: 0.369

Gnomad FIN AF: 0.307

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.330

Gnomad OTH AF: 0.369

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

GnomAD4 genome AF: 0.357 AC: 54215 AN: 151948 Hom.: 9848 Cov.: 32 AF XY: 0.356 AC XY: 26449 AN XY: 74242

African (AFR) AF: 0.408 AC: 16908 AN: 41440

American (AMR) AF: 0.357 AC: 5452 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.287 AC: 994 AN: 3468

East Asian (EAS) AF: 0.437 AC: 2258 AN: 5162

South Asian (SAS) AF: 0.369 AC: 1776 AN: 4818

European-Finnish (FIN) AF: 0.307 AC: 3227 AN: 10528

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.330 AC: 22438 AN: 67952

Other (OTH) AF: 0.370 AC: 780 AN: 2106

Alfa AF: 0.345 Hom.: 5556

Bravo AF: 0.362

Asia WGS AF: 0.448 AC: 1558 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	8.0
DANN	Benign	0.43
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs4379175; hg19: chr5-158804928;