ENST00000740909.1:n.1004T>C

Variant names:

• chr22-48345986-A-G
• rs4407
• ENST00000740909.1:n.1004T>C

Variant summary

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

The ENST00000740909.1(ENSG00000296627):​n.1004T>C 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 0.328 in 152,152 control chromosomes in the GnomAD database, including 9,020 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 0.33 (9020 hom., cov: 34)
• Consequence: ENSG00000296627 ENST00000740909.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.87
• Publications: 10 publications found

Genes affected

ENSG00000296627 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.389 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
ENSG00000296627	ENST00000740909.1	n.1004T>C		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.328 AC: 49850 AN: 152034 Hom.: 9015 Cov.: 34

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.451

Gnomad AMR AF: 0.397

Gnomad ASJ AF: 0.380

Gnomad EAS AF: 0.309

Gnomad SAS AF: 0.404

Gnomad FIN AF: 0.425

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.389

Gnomad OTH AF: 0.335

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

GnomAD4 genome AF: 0.328 AC: 49891 AN: 152152 Hom.: 9020 Cov.: 34 AF XY: 0.331 AC XY: 24598 AN XY: 74370

African (AFR) AF: 0.163 AC: 6777 AN: 41534

American (AMR) AF: 0.397 AC: 6068 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.380 AC: 1316 AN: 3466

East Asian (EAS) AF: 0.309 AC: 1594 AN: 5156

South Asian (SAS) AF: 0.403 AC: 1947 AN: 4826

European-Finnish (FIN) AF: 0.425 AC: 4496 AN: 10574

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.389 AC: 26475 AN: 67984

Other (OTH) AF: 0.338 AC: 715 AN: 2116

Alfa AF: 0.369 Hom.: 16296

Bravo AF: 0.318

Asia WGS AF: 0.364 AC: 1264 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.26
DANN	Benign	0.33
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs4407; hg19: chr22-48741798;