ENST00000594927.1:n.1438G>A

Variant names:

• chr19-21592569-C-T
• rs8112960
• ENST00000594927.2:n.1438G>A

Variant summary

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

The ENST00000594927.2(ENSG00000268240):​n.1438G>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 0.323 in 152,086 control chromosomes in the GnomAD database, including 8,171 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 0.32 (8168 hom., cov: 32)
  • Exomes 𝑓: 0.32 (3 hom.)
• Consequence: ENSG00000268240 ENST00000594927.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0760
• Publications: 29 publications found

Genes affected

ENSG00000268240 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.388 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000594927.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000268240	ENST00000594927.2	TSL:1	n.1438G>A		non_coding_transcript_exon	Exon 1 of 2
	ENSG00000268240	ENST00000789632.1		n.310G>A		non_coding_transcript_exon	Exon 3 of 4
	ENSG00000268240	ENST00000789636.1		n.297G>A		non_coding_transcript_exon	Exon 3 of 4

Frequencies

GnomAD3 genomes AF: 0.324 AC: 49156 AN: 151896 Hom.: 8165 Cov.: 32

Gnomad AFR AF: 0.256

Gnomad AMI AF: 0.343

Gnomad AMR AF: 0.367

Gnomad ASJ AF: 0.377

Gnomad EAS AF: 0.402

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.353

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.341

Gnomad OTH AF: 0.344

GnomAD4 exome AF: 0.319 AC: 23 AN: 72 Hom.: 3 Cov.: 0 AF XY: 0.310 AC XY: 18 AN XY: 58

African (AFR) AF: 0.00 AC: 0 AN: 4

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 1 AN: 2

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 0.167 AC: 1 AN: 6

European-Finnish (FIN) AF: 0.333 AC: 2 AN: 6

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.386 AC: 17 AN: 44

Other (OTH) AF: 0.200 AC: 2 AN: 10

GnomAD4 genome AF: 0.323 AC: 49174 AN: 152014 Hom.: 8168 Cov.: 32 AF XY: 0.326 AC XY: 24198 AN XY: 74286

African (AFR) AF: 0.256 AC: 10619 AN: 41460

American (AMR) AF: 0.367 AC: 5612 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.377 AC: 1306 AN: 3464

East Asian (EAS) AF: 0.403 AC: 2069 AN: 5140

South Asian (SAS) AF: 0.315 AC: 1517 AN: 4822

European-Finnish (FIN) AF: 0.353 AC: 3730 AN: 10564

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.341 AC: 23188 AN: 67964

Other (OTH) AF: 0.340 AC: 718 AN: 2114

Alfa AF: 0.336 Hom.: 27192

Bravo AF: 0.323

Asia WGS AF: 0.289 AC: 1006 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.5
DANN	Benign	0.33
PhyloP100		0.076

Splicing

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

Other links and lift over

dbSNP: rs8112960; hg19: chr19-21775371;