5-54902947-T-C

Variant names:

• chr5-54902947-T-C
• rs4242051
• ENST00000736670.1:n.372-35903A>G

Variant summary

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

The ENST00000736670.1(ENSG00000296132):​n.372-35903A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.77 in 152,106 control chromosomes in the GnomAD database, including 45,210 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 0.77 (45210 hom., cov: 32)
• Consequence: ENSG00000296132 ENST00000736670.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.425
• Publications: 5 publications found

Genes affected

ENSG00000296132 (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 (AFR) allele frequency at 95% confidence interval = 0.8 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
ENSG00000296132	ENST00000736670.1	n.372-35903A>G		intron_variant	Intron 1 of 1
ENSG00000296132	ENST00000736672.1	n.228+7481A>G		intron_variant	Intron 1 of 1
ENSG00000296132	ENST00000736673.1	n.143+7481A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.770 AC: 116971 AN: 151988 Hom.: 45172 Cov.: 32

Gnomad AFR AF: 0.808

Gnomad AMI AF: 0.633

Gnomad AMR AF: 0.796

Gnomad ASJ AF: 0.758

Gnomad EAS AF: 0.656

Gnomad SAS AF: 0.747

Gnomad FIN AF: 0.763

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.755

Gnomad OTH AF: 0.764

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

GnomAD4 genome AF: 0.770 AC: 117060 AN: 152106 Hom.: 45210 Cov.: 32 AF XY: 0.769 AC XY: 57130 AN XY: 74332

African (AFR) AF: 0.808 AC: 33514 AN: 41502

American (AMR) AF: 0.797 AC: 12181 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.758 AC: 2631 AN: 3472

East Asian (EAS) AF: 0.655 AC: 3388 AN: 5172

South Asian (SAS) AF: 0.746 AC: 3597 AN: 4822

European-Finnish (FIN) AF: 0.763 AC: 8057 AN: 10560

Middle Eastern (MID) AF: 0.728 AC: 214 AN: 294

European-Non Finnish (NFE) AF: 0.755 AC: 51292 AN: 67974

Other (OTH) AF: 0.763 AC: 1610 AN: 2110

Alfa AF: 0.754 Hom.: 14081

Bravo AF: 0.774

Asia WGS AF: 0.723 AC: 2513 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	3.2
DANN	Benign	0.79
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs4242051; hg19: chr5-54198775;