ENST00000400933.2:n.596G>A

Variant names:

• chr1-247184887-C-T
• rs3738443
• ENST00000400933.2:n.596G>A

Variant summary

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

The ENST00000400933.2(ENSG00000215795):​n.596G>A 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 0.169 in 589,398 control chromosomes in the GnomAD database, including 10,531 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 0.13 (1717 hom., cov: 32)
  • Exomes 𝑓: 0.18 (8814 hom.)
• Consequence: ENSG00000215795 ENST00000400933.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.312
• Publications: 12 publications found

Genes affected

ENSG00000215795 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (SAS) 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
LOC100131465		n.247184887C>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000215795	ENST00000400933.2	n.596G>A		non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000305271	ENST00000809956.1	n.734-297C>T		intron_variant	Intron 5 of 5
ENSG00000305271	ENST00000809957.1	n.714-297C>T		intron_variant	Intron 5 of 5
ENSG00000305271	ENST00000809958.1	n.453-297C>T		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.132 AC: 20052 AN: 152098 Hom.: 1716 Cov.: 32

Gnomad AFR AF: 0.0319

Gnomad AMI AF: 0.158

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.184

Gnomad EAS AF: 0.204

Gnomad SAS AF: 0.329

Gnomad FIN AF: 0.174

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.165

Gnomad OTH AF: 0.145

GnomAD4 exome AF: 0.183 AC: 79787 AN: 437182 Hom.: 8814 Cov.: 0 AF XY: 0.197 AC XY: 47813 AN XY: 243088

African (AFR) AF: 0.0293 AC: 377 AN: 12868

American (AMR) AF: 0.107 AC: 3990 AN: 37136

Ashkenazi Jewish (ASJ) AF: 0.187 AC: 2490 AN: 13288

East Asian (EAS) AF: 0.220 AC: 4244 AN: 19266

South Asian (SAS) AF: 0.338 AC: 21264 AN: 62884

European-Finnish (FIN) AF: 0.162 AC: 5727 AN: 35296

Middle Eastern (MID) AF: 0.253 AC: 549 AN: 2166

European-Non Finnish (NFE) AF: 0.162 AC: 37676 AN: 232658

Other (OTH) AF: 0.161 AC: 3470 AN: 21620

GnomAD4 genome AF: 0.132 AC: 20052 AN: 152216 Hom.: 1717 Cov.: 32 AF XY: 0.136 AC XY: 10104 AN XY: 74404

African (AFR) AF: 0.0318 AC: 1321 AN: 41560

American (AMR) AF: 0.122 AC: 1865 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.184 AC: 640 AN: 3470

East Asian (EAS) AF: 0.205 AC: 1059 AN: 5162

South Asian (SAS) AF: 0.330 AC: 1592 AN: 4826

European-Finnish (FIN) AF: 0.174 AC: 1840 AN: 10590

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.165 AC: 11223 AN: 67992

Other (OTH) AF: 0.143 AC: 302 AN: 2114

Alfa AF: 0.140 Hom.: 1571

Bravo AF: 0.122

Asia WGS AF: 0.203 AC: 707 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	3.3
DANN	Benign	0.60
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs3738443; hg19: chr1-247348189; COSMIC: COSV68931107;