chr7-128238214-T-C

Variant names:

• chr7-128238214-T-C
• rs11770725
• ENST00000785131.1:n.169-16674A>G

Variant summary

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

The ENST00000785131.1(ENSG00000289434):​n.169-16674A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.446 in 152,122 control chromosomes in the GnomAD database, including 17,974 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 (17974 hom., cov: 33)
• Consequence: ENSG00000289434 ENST00000785131.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.781
• 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.726 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.169-16674A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.447 AC: 67890 AN: 152004 Hom.: 17970 Cov.: 33

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.646

Gnomad AMR AF: 0.513

Gnomad ASJ AF: 0.527

Gnomad EAS AF: 0.744

Gnomad SAS AF: 0.643

Gnomad FIN AF: 0.561

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.553

Gnomad OTH AF: 0.473

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

GnomAD4 genome AF: 0.446 AC: 67908 AN: 152122 Hom.: 17974 Cov.: 33 AF XY: 0.455 AC XY: 33804 AN XY: 74342

African (AFR) AF: 0.145 AC: 6020 AN: 41506

American (AMR) AF: 0.513 AC: 7848 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.527 AC: 1831 AN: 3472

East Asian (EAS) AF: 0.745 AC: 3862 AN: 5182

South Asian (SAS) AF: 0.643 AC: 3102 AN: 4824

European-Finnish (FIN) AF: 0.561 AC: 5919 AN: 10552

Middle Eastern (MID) AF: 0.551 AC: 162 AN: 294

European-Non Finnish (NFE) AF: 0.553 AC: 37569 AN: 67974

Other (OTH) AF: 0.476 AC: 1006 AN: 2112

Alfa AF: 0.462 Hom.: 2346

Bravo AF: 0.425

Asia WGS AF: 0.669 AC: 2321 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.69
DANN	Benign	0.41
PhyloP100		-0.78

Splicing

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

Other links and lift over

dbSNP: rs11770725; hg19: chr7-127878267;