ENST00000557251.1:n.202A>G

Variant names:

• chr14-42703140-A-G
• rs1698534
• ENST00000557251.1:n.202A>G

Variant summary

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

The ENST00000557251.1(ENSG00000258394):​n.202A>G 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 0.756 in 151,938 control chromosomes in the GnomAD database, including 43,797 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 0.76 (43797 hom., cov: 30)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000258394 ENST00000557251.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.62
• Publications: 2 publications found

Genes affected

ENSG00000258394 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.79 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
ENSG00000258394	ENST00000557251.1	n.202A>G		non_coding_transcript_exon_variant	Exon 3 of 4	5

Frequencies

GnomAD3 genomes AF: 0.756 AC: 114715 AN: 151820 Hom.: 43754 Cov.: 30

Gnomad AFR AF: 0.683

Gnomad AMI AF: 0.791

Gnomad AMR AF: 0.796

Gnomad ASJ AF: 0.773

Gnomad EAS AF: 0.556

Gnomad SAS AF: 0.695

Gnomad FIN AF: 0.840

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.795

Gnomad OTH AF: 0.765

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.756 AC: 114818 AN: 151938 Hom.: 43797 Cov.: 30 AF XY: 0.756 AC XY: 56149 AN XY: 74232

African (AFR) AF: 0.684 AC: 28337 AN: 41442

American (AMR) AF: 0.797 AC: 12151 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.773 AC: 2681 AN: 3470

East Asian (EAS) AF: 0.555 AC: 2856 AN: 5144

South Asian (SAS) AF: 0.695 AC: 3352 AN: 4822

European-Finnish (FIN) AF: 0.840 AC: 8855 AN: 10546

Middle Eastern (MID) AF: 0.721 AC: 212 AN: 294

European-Non Finnish (NFE) AF: 0.795 AC: 54035 AN: 67948

Other (OTH) AF: 0.767 AC: 1619 AN: 2110

Alfa AF: 0.762 Hom.: 27374

Bravo AF: 0.749

Asia WGS AF: 0.686 AC: 2387 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.024
DANN	Benign	0.34
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs1698534; hg19: chr14-43172343;