ENST00000430931.1:n.95A>C

Variant names:

• chr6-78813209-T-G
• rs9361448
• ENST00000430931.1:n.95A>C

Variant summary

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

The ENST00000430931.1(ENSG00000229495):​n.95A>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 0.758 in 145,004 control chromosomes in the GnomAD database, including 44,758 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 (44758 hom., cov: 28)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000229495 ENST00000430931.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.139

Genes affected

ENSG00000229495 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.848 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
ENSG00000229495	ENST00000430931.1	n.95A>C		non_coding_transcript_exon_variant	Exon 1 of 2	5

Frequencies

GnomAD3 genomes AF: 0.758 AC: 109756 AN: 144882 Hom.: 44725 Cov.: 28

Gnomad AFR AF: 0.704

Gnomad AMI AF: 0.763

Gnomad AMR AF: 0.820

Gnomad ASJ AF: 0.723

Gnomad EAS AF: 0.862

Gnomad SAS AF: 0.870

Gnomad FIN AF: 0.772

Gnomad MID AF: 0.713

Gnomad NFE AF: 0.760

Gnomad OTH AF: 0.757

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

GnomAD4 genome AF: 0.758 AC: 109843 AN: 145004 Hom.: 44758 Cov.: 28 AF XY: 0.762 AC XY: 53684 AN XY: 70430

Gnomad4 AFR AF: 0.704

Gnomad4 AMR AF: 0.820

Gnomad4 ASJ AF: 0.723

Gnomad4 EAS AF: 0.862

Gnomad4 SAS AF: 0.871

Gnomad4 FIN AF: 0.772

Gnomad4 NFE AF: 0.760

Gnomad4 OTH AF: 0.760

Alfa AF: 0.764 Hom.: 32549

Asia WGS AF: 0.854 AC: 2915 AN: 3414

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.4
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9361448; hg19: chr6-79522926;