7-128208521-C-G

Variant names:

• chr7-128208521-C-G
• rs2060736
• ENST00000765690.1:n.1166C>G

Variant summary

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

The ENST00000765690.1(ENSG00000292309):​n.1166C>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 0.779 in 152,174 control chromosomes in the GnomAD database, including 47,343 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 0.78 (47343 hom., cov: 33)
• Consequence: ENSG00000292309 ENST00000765690.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00700
• Publications: 2 publications found

Genes affected

ENSG00000292309 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.893 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901744	XR_007060516.1	n.780+1446C>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000292309	ENST00000765690.1	n.1166C>G		non_coding_transcript_exon_variant	Exon 5 of 5
ENSG00000292309	ENST00000765691.1	n.1075C>G		non_coding_transcript_exon_variant	Exon 4 of 4
ENSG00000292309	ENST00000765694.1	n.1263C>G		non_coding_transcript_exon_variant	Exon 4 of 4

Frequencies

GnomAD3 genomes AF: 0.779 AC: 118524 AN: 152058 Hom.: 47338 Cov.: 33

Gnomad AFR AF: 0.599

Gnomad AMI AF: 0.811

Gnomad AMR AF: 0.745

Gnomad ASJ AF: 0.836

Gnomad EAS AF: 0.915

Gnomad SAS AF: 0.769

Gnomad FIN AF: 0.887

Gnomad MID AF: 0.854

Gnomad NFE AF: 0.866

Gnomad OTH AF: 0.803

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.779 AC: 118560 AN: 152174 Hom.: 47343 Cov.: 33 AF XY: 0.780 AC XY: 58034 AN XY: 74396

African (AFR) AF: 0.598 AC: 24810 AN: 41470

American (AMR) AF: 0.745 AC: 11391 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.836 AC: 2903 AN: 3472

East Asian (EAS) AF: 0.915 AC: 4737 AN: 5178

South Asian (SAS) AF: 0.770 AC: 3712 AN: 4820

European-Finnish (FIN) AF: 0.887 AC: 9397 AN: 10600

Middle Eastern (MID) AF: 0.847 AC: 249 AN: 294

European-Non Finnish (NFE) AF: 0.866 AC: 58923 AN: 68020

Other (OTH) AF: 0.805 AC: 1698 AN: 2110

Alfa AF: 0.780 Hom.: 2602

Bravo AF: 0.761

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.8
DANN	Benign	0.47
PhyloP100		-0.0070

Splicing

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

Other links and lift over

dbSNP: rs2060736; hg19: chr7-127848574;