4-73876266-C-T

Variant names:

• chr4-73876266-C-T
• rs4422395
• ENST00000791553.1:n.8C>T

Variant summary

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

The ENST00000791553.1(ENSG00000303067):​n.8C>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 0.18 in 152,046 control chromosomes in the GnomAD database, including 2,849 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 (2849 hom., cov: 32)
• Consequence: ENSG00000303067 ENST00000791553.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.527
• Publications: 5 publications found

Genes affected

ENSG00000303067 (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 = 0.316 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
ENSG00000303067	ENST00000791553.1	n.8C>T		non_coding_transcript_exon_variant	Exon 1 of 3
ENSG00000303067	ENST00000791548.1	n.122+2328C>T		intron_variant	Intron 2 of 2
ENSG00000303067	ENST00000791549.1	n.64+2328C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.180 AC: 27315 AN: 151926 Hom.: 2837 Cov.: 32

Gnomad AFR AF: 0.116

Gnomad AMI AF: 0.201

Gnomad AMR AF: 0.323

Gnomad ASJ AF: 0.259

Gnomad EAS AF: 0.274

Gnomad SAS AF: 0.176

Gnomad FIN AF: 0.205

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.209

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

GnomAD4 genome AF: 0.180 AC: 27344 AN: 152046 Hom.: 2849 Cov.: 32 AF XY: 0.185 AC XY: 13725 AN XY: 74334

African (AFR) AF: 0.116 AC: 4805 AN: 41500

American (AMR) AF: 0.324 AC: 4940 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.259 AC: 898 AN: 3470

East Asian (EAS) AF: 0.275 AC: 1413 AN: 5142

South Asian (SAS) AF: 0.176 AC: 851 AN: 4822

European-Finnish (FIN) AF: 0.205 AC: 2164 AN: 10580

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.170 AC: 11585 AN: 67962

Other (OTH) AF: 0.207 AC: 436 AN: 2110

Alfa AF: 0.186 Hom.: 739

Bravo AF: 0.190

Asia WGS AF: 0.211 AC: 735 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.5
DANN	Benign	0.64
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs4422395; hg19: chr4-74741983;