5-75742893-C-G

Variant names:

• chr5-75742893-C-G
• rs258494
• ENST00000814440.1:n.236-3209C>G

Variant summary

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

The ENST00000814440.1(ENSG00000305970):​n.236-3209C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.555 in 151,842 control chromosomes in the GnomAD database, including 23,988 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 0.56 (23988 hom., cov: 30)
• Consequence: ENSG00000305970 ENST00000814440.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0460
• Publications: 10 publications found

Genes affected

ENSG00000305970 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.623 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
ENSG00000305970	ENST00000814440.1	n.236-3209C>G		intron_variant	Intron 2 of 4
ENSG00000305970	ENST00000814441.1	n.233-3206C>G		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.555 AC: 84268 AN: 151724 Hom.: 23980 Cov.: 30

Gnomad AFR AF: 0.420

Gnomad AMI AF: 0.523

Gnomad AMR AF: 0.578

Gnomad ASJ AF: 0.576

Gnomad EAS AF: 0.494

Gnomad SAS AF: 0.590

Gnomad FIN AF: 0.578

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.628

Gnomad OTH AF: 0.596

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

GnomAD4 genome AF: 0.555 AC: 84320 AN: 151842 Hom.: 23988 Cov.: 30 AF XY: 0.554 AC XY: 41082 AN XY: 74222

African (AFR) AF: 0.421 AC: 17397 AN: 41370

American (AMR) AF: 0.578 AC: 8824 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.576 AC: 1995 AN: 3464

East Asian (EAS) AF: 0.495 AC: 2553 AN: 5162

South Asian (SAS) AF: 0.590 AC: 2840 AN: 4814

European-Finnish (FIN) AF: 0.578 AC: 6077 AN: 10510

Middle Eastern (MID) AF: 0.690 AC: 203 AN: 294

European-Non Finnish (NFE) AF: 0.628 AC: 42691 AN: 67944

Other (OTH) AF: 0.598 AC: 1263 AN: 2112

Alfa AF: 0.471 Hom.: 1438

Bravo AF: 0.550

Asia WGS AF: 0.553 AC: 1925 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.86
DANN	Benign	0.35
PhyloP100		-0.046

Splicing

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

Other links and lift over

dbSNP: rs258494; hg19: chr5-75038718;