7-129604824-T-C

Position:

• chr7-129604824-T-C

Variant summary

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

The ENST00000608694.2(ENSG00000273329):​n.6848A>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 0.883 in 152,158 control chromosomes in the GnomAD database, including 59,532 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 0.88 (59532 hom., cov: 31)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000273329 ENST00000608694.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0710

Genes affected

ENSG00000273329 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.911 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.129604824T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000273329	ENST00000608694.2	n.6848A>G		non_coding_transcript_exon_variant	1/1	6

Frequencies

GnomAD3 genomes AF: 0.883 AC: 134311 AN: 152040 Hom.: 59500 Cov.: 31

Gnomad AFR AF: 0.816

Gnomad AMI AF: 0.915

Gnomad AMR AF: 0.891

Gnomad ASJ AF: 0.896

Gnomad EAS AF: 0.933

Gnomad SAS AF: 0.922

Gnomad FIN AF: 0.897

Gnomad MID AF: 0.880

Gnomad NFE AF: 0.914

Gnomad OTH AF: 0.863

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: 0.883 AC: 134395 AN: 152158 Hom.: 59532 Cov.: 31 AF XY: 0.885 AC XY: 65826 AN XY: 74392

Gnomad4 AFR AF: 0.815

Gnomad4 AMR AF: 0.891

Gnomad4 ASJ AF: 0.896

Gnomad4 EAS AF: 0.933

Gnomad4 SAS AF: 0.923

Gnomad4 FIN AF: 0.897

Gnomad4 NFE AF: 0.914

Gnomad4 OTH AF: 0.865

Alfa AF: 0.901 Hom.: 20228

Bravo AF: 0.877

Asia WGS AF: 0.880 AC: 3061 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.2
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9792084; hg19: chr7-129244665;