ENST00000436510.1:n.1791T>C

Variant names:

• chr9-129430707-A-G
• rs4837366
• ENST00000436510.1:n.1791T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000436510.1(ENSG00000230676):​n.1791T>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 0.198 in 140,200 control chromosomes in the GnomAD database, including 934 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 0.20 (934 hom., cov: 45)
  • Exomes 𝑓: 0.31 (0 hom.)
• Consequence: ENSG00000230676 ENST00000436510.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.178

Genes affected

ENSG00000230676 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 = 0.372 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
ENSG00000230676	ENST00000436510.1	n.1791T>C		non_coding_transcript_exon_variant	Exon 2 of 2	5

Frequencies

GnomAD3 genomes AF: 0.198 AC: 27679 AN: 140068 Hom.: 931 Cov.: 45

Gnomad AFR AF: 0.102

Gnomad AMI AF: 0.210

Gnomad AMR AF: 0.304

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.386

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.231

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.223

GnomAD4 exome AF: 0.313 AC: 5 AN: 16 Hom.: 0 Cov.: 0 AF XY: 0.375 AC XY: 3 AN XY: 8

Gnomad4 FIN exome AF: 0.375

Gnomad4 NFE exome AF: 0.167

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.198 AC: 27692 AN: 140184 Hom.: 934 Cov.: 45 AF XY: 0.201 AC XY: 13689 AN XY: 68248

Gnomad4 AFR AF: 0.102

Gnomad4 AMR AF: 0.304

Gnomad4 ASJ AF: 0.178

Gnomad4 EAS AF: 0.387

Gnomad4 SAS AF: 0.227

Gnomad4 FIN AF: 0.231

Gnomad4 NFE AF: 0.209

Gnomad4 OTH AF: 0.225

Alfa AF: 0.211 Hom.: 7003

Asia WGS AF: 0.324 AC: 1122 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.8
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4837366; hg19: chr9-132192986;