rs1074442

Variant names:

• chr4-183573618-T-A
• rs1074442
• ENST00000732331.1:n.204-5295A>T

Your query was ambiguous. Multiple possible variants found:

• chr4-183573618-T-A
• chr4-183573618-T-C

Variant summary

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

The ENST00000732331.1(ENSG00000295742):​n.204-5295A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.185 in 151,952 control chromosomes in the GnomAD database, including 2,774 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 0.18 (2774 hom., cov: 32)
• Consequence: ENSG00000295742 ENST00000732331.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308
• Publications: 0 publications found

Genes affected

ENSG00000295742 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.352 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
ENSG00000295742	ENST00000732331.1	n.204-5295A>T		intron_variant	Intron 1 of 1
ENSG00000295742	ENST00000732332.1	n.149-5295A>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.184 AC: 28000 AN: 151834 Hom.: 2767 Cov.: 32

Gnomad AFR AF: 0.222

Gnomad AMI AF: 0.0802

Gnomad AMR AF: 0.230

Gnomad ASJ AF: 0.0756

Gnomad EAS AF: 0.366

Gnomad SAS AF: 0.157

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.196

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

GnomAD4 genome AF: 0.185 AC: 28039 AN: 151952 Hom.: 2774 Cov.: 32 AF XY: 0.186 AC XY: 13838 AN XY: 74280

African (AFR) AF: 0.222 AC: 9195 AN: 41438

American (AMR) AF: 0.230 AC: 3510 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0756 AC: 262 AN: 3464

East Asian (EAS) AF: 0.366 AC: 1882 AN: 5142

South Asian (SAS) AF: 0.158 AC: 759 AN: 4814

European-Finnish (FIN) AF: 0.159 AC: 1681 AN: 10550

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.150 AC: 10226 AN: 67956

Other (OTH) AF: 0.202 AC: 427 AN: 2114

Alfa AF: 0.162 Hom.: 240

Bravo AF: 0.195

Asia WGS AF: 0.270 AC: 937 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.3
DANN	Benign	0.28
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs1074442; hg19: chr4-184494771;