7-128235336-T-G

Variant names:

• chr7-128235336-T-G
• rs4731424
• ENST00000785133.1:n.923A>C

Variant summary

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

The ENST00000785133.1(ENSG00000289434):​n.923A>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 0.785 in 152,198 control chromosomes in the GnomAD database, including 50,389 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 (50389 hom., cov: 34)
• Consequence: ENSG00000289434 ENST00000785133.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.443
• Publications: 2 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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.922 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000785133.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000289434	ENST00000785133.1		n.923A>C		non_coding_transcript_exon	Exon 3 of 3
	ENSG00000289434	ENST00000690022.2		n.288+922A>C		intron	N/A
	ENSG00000289434	ENST00000692614.3		n.527+922A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.785 AC: 119382 AN: 152080 Hom.: 50368 Cov.: 34

Gnomad AFR AF: 0.440

Gnomad AMI AF: 0.958

Gnomad AMR AF: 0.883

Gnomad ASJ AF: 0.876

Gnomad EAS AF: 0.944

Gnomad SAS AF: 0.936

Gnomad FIN AF: 0.904

Gnomad MID AF: 0.911

Gnomad NFE AF: 0.923

Gnomad OTH AF: 0.811

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

GnomAD4 genome AF: 0.785 AC: 119445 AN: 152198 Hom.: 50389 Cov.: 34 AF XY: 0.791 AC XY: 58865 AN XY: 74434

African (AFR) AF: 0.440 AC: 18259 AN: 41460

American (AMR) AF: 0.883 AC: 13516 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.876 AC: 3043 AN: 3472

East Asian (EAS) AF: 0.944 AC: 4889 AN: 5180

South Asian (SAS) AF: 0.937 AC: 4522 AN: 4828

European-Finnish (FIN) AF: 0.904 AC: 9594 AN: 10614

Middle Eastern (MID) AF: 0.901 AC: 265 AN: 294

European-Non Finnish (NFE) AF: 0.923 AC: 62771 AN: 68024

Other (OTH) AF: 0.812 AC: 1712 AN: 2108

Alfa AF: 0.836 Hom.: 6912

Bravo AF: 0.768

Asia WGS AF: 0.904 AC: 3140 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.6
DANN	Benign	0.55
PhyloP100		-0.44

Splicing

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

Other links and lift over

dbSNP: rs4731424; hg19: chr7-127875389;