chr7-129604824-T-C

Variant names:

• chr7-129604824-T-C
• rs9792084
• ENST00000608694.3:n.6852A>G

Variant summary

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

The ENST00000608694.3(ENSG00000273329):​n.6852A>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 ENST00000608694.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0710
• Publications: 5 publications found

Genes affected

ENSG00000273329 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000608694.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000273329	ENST00000608694.3	TSL:6	n.6852A>G		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000273329	ENST00000786136.1		n.622+2132A>G		intron	N/A
	ENSG00000273329	ENST00000786137.1		n.343+6494A>G		intron	N/A

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

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

African (AFR) AF: 0.815 AC: 33812 AN: 41472

American (AMR) AF: 0.891 AC: 13611 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.896 AC: 3110 AN: 3472

East Asian (EAS) AF: 0.933 AC: 4835 AN: 5180

South Asian (SAS) AF: 0.923 AC: 4451 AN: 4824

European-Finnish (FIN) AF: 0.897 AC: 9513 AN: 10600

Middle Eastern (MID) AF: 0.881 AC: 259 AN: 294

European-Non Finnish (NFE) AF: 0.914 AC: 62143 AN: 68012

Other (OTH) AF: 0.865 AC: 1828 AN: 2114

Alfa AF: 0.901 Hom.: 23402

Bravo AF: 0.877

Asia WGS AF: 0.880 AC: 3061 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.2
DANN	Benign	0.56
PhyloP100		-0.071

Splicing

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

Other links and lift over

dbSNP: rs9792084; hg19: chr7-129244665;