7-128222749-A-G

Variant names:

• chr7-128222749-A-G
• rs791595
• ENST00000690022.2:n.289-1209T>C

Variant summary

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

The ENST00000690022.2(ENSG00000289434):​n.289-1209T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.761 in 152,140 control chromosomes in the GnomAD database, including 44,746 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 (44746 hom., cov: 32)
• Consequence: ENSG00000289434 ENST00000690022.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.30
• Publications: 45 publications found

Genes affected

ENSG00000289434 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.858 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000690022.2. 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
	ENSG00000289434	ENST00000690022.2		n.289-1209T>C		intron	N/A
	ENSG00000289434	ENST00000692614.3		n.528-1209T>C		intron	N/A
	ENSG00000292309	ENST00000710955.1		n.836-1284A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.761 AC: 115707 AN: 152022 Hom.: 44713 Cov.: 32

Gnomad AFR AF: 0.611

Gnomad AMI AF: 0.890

Gnomad AMR AF: 0.827

Gnomad ASJ AF: 0.796

Gnomad EAS AF: 0.879

Gnomad SAS AF: 0.799

Gnomad FIN AF: 0.825

Gnomad MID AF: 0.713

Gnomad NFE AF: 0.813

Gnomad OTH AF: 0.765

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

GnomAD4 genome AF: 0.761 AC: 115789 AN: 152140 Hom.: 44746 Cov.: 32 AF XY: 0.764 AC XY: 56843 AN XY: 74376

African (AFR) AF: 0.610 AC: 25322 AN: 41482

American (AMR) AF: 0.827 AC: 12650 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.796 AC: 2762 AN: 3472

East Asian (EAS) AF: 0.879 AC: 4552 AN: 5176

South Asian (SAS) AF: 0.800 AC: 3849 AN: 4814

European-Finnish (FIN) AF: 0.825 AC: 8745 AN: 10594

Middle Eastern (MID) AF: 0.709 AC: 207 AN: 292

European-Non Finnish (NFE) AF: 0.813 AC: 55268 AN: 67990

Other (OTH) AF: 0.767 AC: 1622 AN: 2114

Alfa AF: 0.794 Hom.: 153338

Bravo AF: 0.755

Asia WGS AF: 0.847 AC: 2940 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	13
DANN	Benign	0.36
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs791595; hg19: chr7-127862802;