rs4875598

Variant names:

• chr8-5604231-G-A
• rs4875598
• ENST00000807442.1:n.94C>T

Your query was ambiguous. Multiple possible variants found:

• chr8-5604231-G-A
• chr8-5604231-G-C

Variant summary

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

The ENST00000807442.1(ENSG00000304969):​n.94C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.643 in 152,064 control chromosomes in the GnomAD database, including 31,582 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 0.64 (31582 hom., cov: 32)
• Consequence: ENSG00000304969 ENST00000807442.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.495
• Publications: 11 publications found

Genes affected

ENSG00000304969 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.733 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
ENSG00000304969	ENST00000807442.1	n.94C>T		non_coding_transcript_exon_variant	Exon 1 of 2
ENSG00000304969	ENST00000807443.1	n.95C>T		non_coding_transcript_exon_variant	Exon 1 of 3
ENSG00000304969	ENST00000807444.1	n.77C>T		non_coding_transcript_exon_variant	Exon 1 of 4

Frequencies

GnomAD3 genomes AF: 0.643 AC: 97739 AN: 151946 Hom.: 31543 Cov.: 32

Gnomad AFR AF: 0.612

Gnomad AMI AF: 0.721

Gnomad AMR AF: 0.743

Gnomad ASJ AF: 0.695

Gnomad EAS AF: 0.655

Gnomad SAS AF: 0.634

Gnomad FIN AF: 0.577

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.647

Gnomad OTH AF: 0.634

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

GnomAD4 genome AF: 0.643 AC: 97828 AN: 152064 Hom.: 31582 Cov.: 32 AF XY: 0.641 AC XY: 47610 AN XY: 74310

African (AFR) AF: 0.612 AC: 25377 AN: 41478

American (AMR) AF: 0.744 AC: 11379 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.695 AC: 2409 AN: 3468

East Asian (EAS) AF: 0.655 AC: 3375 AN: 5150

South Asian (SAS) AF: 0.634 AC: 3054 AN: 4818

European-Finnish (FIN) AF: 0.577 AC: 6086 AN: 10548

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.647 AC: 43975 AN: 67998

Other (OTH) AF: 0.636 AC: 1339 AN: 2104

Alfa AF: 0.644 Hom.: 60820

Bravo AF: 0.656

Asia WGS AF: 0.649 AC: 2254 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.6
DANN	Benign	0.21
PhyloP100		0.49

Splicing

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

Other links and lift over

dbSNP: rs4875598; hg19: chr8-5461753;