rs835141

Variant names:

• chr5-14888399-C-T
• rs835141
• ENST00000749079.1:n.94-433C>T

Variant summary

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

The ENST00000749079.1(ENSG00000297585):​n.94-433C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.536 in 152,090 control chromosomes in the GnomAD database, including 22,045 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 0.54 (22045 hom., cov: 34)
• Consequence: ENSG00000297585 ENST00000749079.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.110
• Publications: 2 publications found

Genes affected

ENSG00000297585 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.584 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
ENSG00000297585	ENST00000749079.1	n.94-433C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.535 AC: 81379 AN: 151972 Hom.: 22007 Cov.: 34

Gnomad AFR AF: 0.590

Gnomad AMI AF: 0.408

Gnomad AMR AF: 0.473

Gnomad ASJ AF: 0.546

Gnomad EAS AF: 0.376

Gnomad SAS AF: 0.349

Gnomad FIN AF: 0.555

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.541

Gnomad OTH AF: 0.504

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

GnomAD4 genome AF: 0.536 AC: 81455 AN: 152090 Hom.: 22045 Cov.: 34 AF XY: 0.530 AC XY: 39380 AN XY: 74338

African (AFR) AF: 0.591 AC: 24499 AN: 41486

American (AMR) AF: 0.472 AC: 7221 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.546 AC: 1893 AN: 3470

East Asian (EAS) AF: 0.377 AC: 1950 AN: 5174

South Asian (SAS) AF: 0.349 AC: 1679 AN: 4814

European-Finnish (FIN) AF: 0.555 AC: 5857 AN: 10552

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.541 AC: 36784 AN: 67992

Other (OTH) AF: 0.499 AC: 1054 AN: 2114

Alfa AF: 0.530 Hom.: 30594

Bravo AF: 0.531

Asia WGS AF: 0.343 AC: 1194 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.1
DANN	Benign	0.55
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs835141; hg19: chr5-14888508;