chr7-128235280-G-A

Variant names:

• chr7-128235280-G-A
• rs4731423
• ENST00000785133.1:n.979C>T

Variant summary

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

The ENST00000785133.1(ENSG00000289434):​n.979C>T 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 0.451 in 152,148 control chromosomes in the GnomAD database, including 18,106 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 0.45 (18106 hom., cov: 33)
• Consequence: ENSG00000289434 ENST00000785133.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.505
• Publications: 8 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.723 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289434	ENST00000785133.1	n.979C>T		non_coding_transcript_exon_variant	Exon 3 of 3
ENSG00000289434	ENST00000690022.2	n.288+978C>T		intron_variant	Intron 2 of 2
ENSG00000289434	ENST00000692614.3	n.527+978C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.452 AC: 68659 AN: 152030 Hom.: 18101 Cov.: 33

Gnomad AFR AF: 0.162

Gnomad AMI AF: 0.646

Gnomad AMR AF: 0.516

Gnomad ASJ AF: 0.532

Gnomad EAS AF: 0.741

Gnomad SAS AF: 0.641

Gnomad FIN AF: 0.562

Gnomad MID AF: 0.564

Gnomad NFE AF: 0.553

Gnomad OTH AF: 0.476

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

GnomAD4 genome AF: 0.451 AC: 68679 AN: 152148 Hom.: 18106 Cov.: 33 AF XY: 0.459 AC XY: 34166 AN XY: 74374

African (AFR) AF: 0.162 AC: 6732 AN: 41520

American (AMR) AF: 0.516 AC: 7881 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.532 AC: 1847 AN: 3470

East Asian (EAS) AF: 0.742 AC: 3837 AN: 5170

South Asian (SAS) AF: 0.642 AC: 3100 AN: 4830

European-Finnish (FIN) AF: 0.562 AC: 5932 AN: 10562

Middle Eastern (MID) AF: 0.555 AC: 162 AN: 292

European-Non Finnish (NFE) AF: 0.553 AC: 37587 AN: 67992

Other (OTH) AF: 0.479 AC: 1012 AN: 2112

Alfa AF: 0.439 Hom.: 2409

Bravo AF: 0.431

Asia WGS AF: 0.663 AC: 2302 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.42
DANN	Benign	0.73
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs4731423; hg19: chr7-127875333;