ENST00000785131.1:n.169-17755A>G

Variant names:

• chr7-128239295-T-C
• rs4728096
• ENST00000785131.1:n.169-17755A>G

Variant summary

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

The ENST00000785131.1(ENSG00000289434):​n.169-17755A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.377 in 152,058 control chromosomes in the GnomAD database, including 11,986 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 0.38 (11986 hom., cov: 31)
• Consequence: ENSG00000289434 ENST00000785131.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214
• Publications: 4 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 (NFE) allele frequency at 95% confidence interval = 0.469 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000785131.1. 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	ENST00000785131.1		n.169-17755A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.377 AC: 57255 AN: 151940 Hom.: 11986 Cov.: 31

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.521

Gnomad AMR AF: 0.432

Gnomad ASJ AF: 0.458

Gnomad EAS AF: 0.201

Gnomad SAS AF: 0.371

Gnomad FIN AF: 0.395

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.474

Gnomad OTH AF: 0.408

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

GnomAD4 genome AF: 0.377 AC: 57280 AN: 152058 Hom.: 11986 Cov.: 31 AF XY: 0.372 AC XY: 27673 AN XY: 74322

African (AFR) AF: 0.203 AC: 8432 AN: 41468

American (AMR) AF: 0.433 AC: 6608 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.458 AC: 1590 AN: 3468

East Asian (EAS) AF: 0.200 AC: 1040 AN: 5188

South Asian (SAS) AF: 0.371 AC: 1787 AN: 4816

European-Finnish (FIN) AF: 0.395 AC: 4174 AN: 10562

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.474 AC: 32183 AN: 67966

Other (OTH) AF: 0.406 AC: 856 AN: 2108

Alfa AF: 0.419 Hom.: 1852

Bravo AF: 0.376

Asia WGS AF: 0.255 AC: 887 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.7
DANN	Benign	0.15
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs4728096; hg19: chr7-127879348;