chr7-128263486-A-G

Variant names:

• chr7-128263486-A-G
• rs4731429
• ENST00000785131.1:n.44T>C

Variant summary

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

The ENST00000785131.1(ENSG00000289434):​n.44T>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 0.435 in 152,116 control chromosomes in the GnomAD database, including 17,118 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 0.44 (17118 hom., cov: 32)
• Consequence: ENSG00000289434 ENST00000785131.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.522
• Publications: 13 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=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.706 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	ENST00000785131.1	n.44T>C		non_coding_transcript_exon_variant	Exon 1 of 2

Frequencies

GnomAD3 genomes AF: 0.435 AC: 66164 AN: 151996 Hom.: 17109 Cov.: 32

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.597

Gnomad AMR AF: 0.515

Gnomad ASJ AF: 0.553

Gnomad EAS AF: 0.724

Gnomad SAS AF: 0.551

Gnomad FIN AF: 0.498

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.545

Gnomad OTH AF: 0.472

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

GnomAD4 genome AF: 0.435 AC: 66177 AN: 152116 Hom.: 17118 Cov.: 32 AF XY: 0.438 AC XY: 32585 AN XY: 74356

African (AFR) AF: 0.143 AC: 5942 AN: 41516

American (AMR) AF: 0.515 AC: 7872 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.553 AC: 1919 AN: 3468

East Asian (EAS) AF: 0.725 AC: 3751 AN: 5172

South Asian (SAS) AF: 0.551 AC: 2657 AN: 4820

European-Finnish (FIN) AF: 0.498 AC: 5259 AN: 10560

Middle Eastern (MID) AF: 0.531 AC: 156 AN: 294

European-Non Finnish (NFE) AF: 0.545 AC: 37071 AN: 67982

Other (OTH) AF: 0.477 AC: 1007 AN: 2110

Alfa AF: 0.511 Hom.: 11407

Bravo AF: 0.420

Asia WGS AF: 0.631 AC: 2190 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	5.1
DANN	Benign	0.39
PhyloP100		0.52

Splicing

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

Other links and lift over

dbSNP: rs4731429; hg19: chr7-127903539;