rs7089063

Variant names:

• chr10-45450941-C-A
• rs7089063
• ENST00000435635.1:n.179+1903G>T

Variant summary

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

The ENST00000435635.1(ENSG00000231964):​n.179+1903G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.258 in 151,484 control chromosomes in the GnomAD database, including 5,287 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 0.26 (5287 hom., cov: 32)
• Consequence: ENSG00000231964 ENST00000435635.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0900
• Publications: 8 publications found

Genes affected

ENSG00000231964 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.323 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000435635.1. 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
	LOC102724323	NR_120674.1		n.179+1903G>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000231964	ENST00000435635.1	TSL:2	n.179+1903G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.258 AC: 39116 AN: 151384 Hom.: 5283 Cov.: 32

Gnomad AFR AF: 0.327

Gnomad AMI AF: 0.235

Gnomad AMR AF: 0.197

Gnomad ASJ AF: 0.177

Gnomad EAS AF: 0.151

Gnomad SAS AF: 0.219

Gnomad FIN AF: 0.298

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.240

Gnomad OTH AF: 0.244

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

GnomAD4 genome AF: 0.258 AC: 39132 AN: 151484 Hom.: 5287 Cov.: 32 AF XY: 0.260 AC XY: 19268 AN XY: 74016

African (AFR) AF: 0.327 AC: 13498 AN: 41258

American (AMR) AF: 0.197 AC: 3012 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.177 AC: 614 AN: 3462

East Asian (EAS) AF: 0.151 AC: 783 AN: 5172

South Asian (SAS) AF: 0.219 AC: 1052 AN: 4812

European-Finnish (FIN) AF: 0.298 AC: 3080 AN: 10344

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.240 AC: 16295 AN: 67870

Other (OTH) AF: 0.241 AC: 507 AN: 2104

Alfa AF: 0.245 Hom.: 1691

Bravo AF: 0.251

Asia WGS AF: 0.204 AC: 706 AN: 3454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.32
DANN	Benign	0.63
PhyloP100		-0.090

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: rs7089063;

hg19: chr10-45946389;