rs13134954

Variant names:

• chr4-99792464-C-A
• rs13134954
• ENST00000795494.1:n.175+29179G>T

Your query was ambiguous. Multiple possible variants found:

• chr4-99792464-C-A
• chr4-99792464-C-G
• chr4-99792464-C-T

Variant summary

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

The ENST00000795494.1(ENSG00000303547):​n.175+29179G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.332 in 151,950 control chromosomes in the GnomAD database, including 8,606 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 (8606 hom., cov: 31)
• Consequence: ENSG00000303547 ENST00000795494.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00100
• Publications: 3 publications found

Genes affected

ENSG00000303547 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.379 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
ENSG00000303547	ENST00000795494.1	n.175+29179G>T		intron_variant	Intron 2 of 2
ENSG00000303547	ENST00000795495.1	n.349+29179G>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.332 AC: 50416 AN: 151832 Hom.: 8587 Cov.: 31

Gnomad AFR AF: 0.281

Gnomad AMI AF: 0.356

Gnomad AMR AF: 0.386

Gnomad ASJ AF: 0.400

Gnomad EAS AF: 0.393

Gnomad SAS AF: 0.206

Gnomad FIN AF: 0.264

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.361

Gnomad OTH AF: 0.373

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

GnomAD4 genome AF: 0.332 AC: 50482 AN: 151950 Hom.: 8606 Cov.: 31 AF XY: 0.328 AC XY: 24337 AN XY: 74270

African (AFR) AF: 0.281 AC: 11636 AN: 41416

American (AMR) AF: 0.387 AC: 5917 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.400 AC: 1386 AN: 3468

East Asian (EAS) AF: 0.393 AC: 2021 AN: 5136

South Asian (SAS) AF: 0.207 AC: 995 AN: 4818

European-Finnish (FIN) AF: 0.264 AC: 2793 AN: 10570

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.361 AC: 24509 AN: 67944

Other (OTH) AF: 0.375 AC: 790 AN: 2108

Alfa AF: 0.355 Hom.: 8654

Bravo AF: 0.342

Asia WGS AF: 0.294 AC: 1022 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.0
DANN	Benign	0.41
PhyloP100		0.0010

Splicing

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

Other links and lift over

dbSNP: rs13134954; hg19: chr4-100713621;