rs9361448

chr6-78813209-T-G

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: ENST00000430931.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.139

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000430931.1	n.95A>C		non_coding_transcript_exon_variant	1/2	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;