7-128239891-A-G

Variant names:

• chr7-128239891-A-G
• rs13228377
• ENST00000785131.1:n.169-18351T>C

Variant summary

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

The ENST00000785131.1(ENSG00000289434):​n.169-18351T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.397 in 151,886 control chromosomes in the GnomAD database, including 12,775 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 0.40 (12775 hom., cov: 32)
• Consequence: ENSG00000289434 ENST00000785131.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.672
• Publications: 10 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=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.471 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

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	ENST00000785131.1		n.169-18351T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.397 AC: 60262 AN: 151770 Hom.: 12774 Cov.: 32

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.521

Gnomad AMR AF: 0.443

Gnomad ASJ AF: 0.493

Gnomad EAS AF: 0.255

Gnomad SAS AF: 0.391

Gnomad FIN AF: 0.395

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.475

Gnomad OTH AF: 0.436

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

GnomAD4 genome AF: 0.397 AC: 60294 AN: 151886 Hom.: 12775 Cov.: 32 AF XY: 0.392 AC XY: 29130 AN XY: 74252

African (AFR) AF: 0.257 AC: 10651 AN: 41392

American (AMR) AF: 0.444 AC: 6766 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.493 AC: 1712 AN: 3472

East Asian (EAS) AF: 0.254 AC: 1311 AN: 5170

South Asian (SAS) AF: 0.391 AC: 1881 AN: 4816

European-Finnish (FIN) AF: 0.395 AC: 4165 AN: 10536

Middle Eastern (MID) AF: 0.473 AC: 138 AN: 292

European-Non Finnish (NFE) AF: 0.475 AC: 32280 AN: 67942

Other (OTH) AF: 0.434 AC: 915 AN: 2110

Alfa AF: 0.371 Hom.: 2436

Bravo AF: 0.398

Asia WGS AF: 0.294 AC: 1024 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.7
DANN	Benign	0.18
PhyloP100		-0.67

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs13228377;

hg19: chr7-127879944;