4-103493791-T-C

Variant names:

• chr4-103493791-T-C
• rs402681
• ENST00000809036.1:n.-244T>C

Variant summary

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

The ENST00000809036.1(ENSG00000305137):​n.-244T>C variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.725 in 152,092 control chromosomes in the GnomAD database, including 40,905 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 0.73 (40905 hom., cov: 32)
• Consequence: ENSG00000305137 ENST00000809036.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308
• Publications: 3 publications found

Genes affected

ENSG00000305137 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.958 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
ENSG00000305137	ENST00000809036.1	n.-244T>C		upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.725 AC: 110196 AN: 151974 Hom.: 40876 Cov.: 32

Gnomad AFR AF: 0.567

Gnomad AMI AF: 0.748

Gnomad AMR AF: 0.797

Gnomad ASJ AF: 0.759

Gnomad EAS AF: 0.981

Gnomad SAS AF: 0.841

Gnomad FIN AF: 0.818

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.761

Gnomad OTH AF: 0.738

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

GnomAD4 genome AF: 0.725 AC: 110272 AN: 152092 Hom.: 40905 Cov.: 32 AF XY: 0.732 AC XY: 54432 AN XY: 74346

African (AFR) AF: 0.567 AC: 23498 AN: 41444

American (AMR) AF: 0.798 AC: 12187 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.759 AC: 2634 AN: 3470

East Asian (EAS) AF: 0.981 AC: 5082 AN: 5182

South Asian (SAS) AF: 0.840 AC: 4054 AN: 4824

European-Finnish (FIN) AF: 0.818 AC: 8662 AN: 10594

Middle Eastern (MID) AF: 0.663 AC: 195 AN: 294

European-Non Finnish (NFE) AF: 0.761 AC: 51719 AN: 67988

Other (OTH) AF: 0.741 AC: 1560 AN: 2106

Alfa AF: 0.750 Hom.: 72405

Bravo AF: 0.717

Asia WGS AF: 0.858 AC: 2983 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	2.6
DANN	Benign	0.78
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs402681; hg19: chr4-104414948;