rs180925

Variant names:

• chr10-113975176-A-C
• rs180925
• ENST00000751600.1:n.127-4524A>C

Your query was ambiguous. Multiple possible variants found:

• chr10-113975176-A-C
• chr10-113975176-A-G
• chr10-113975176-A-T

Variant summary

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

The ENST00000751600.1(ENSG00000297898):​n.127-4524A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.747 in 151,772 control chromosomes in the GnomAD database, including 42,611 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 0.75 (42611 hom., cov: 30)
• Consequence: ENSG00000297898 ENST00000751600.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.08
• Publications: 8 publications found

Genes affected

ENSG00000297898 (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 = 0.767 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000751600.1. 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
	ENSG00000297898	ENST00000751600.1		n.127-4524A>C		intron	N/A
	ENSG00000297898	ENST00000751601.1		n.59-4524A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.747 AC: 113289 AN: 151652 Hom.: 42559 Cov.: 30

Gnomad AFR AF: 0.774

Gnomad AMI AF: 0.811

Gnomad AMR AF: 0.729

Gnomad ASJ AF: 0.594

Gnomad EAS AF: 0.587

Gnomad SAS AF: 0.724

Gnomad FIN AF: 0.879

Gnomad MID AF: 0.631

Gnomad NFE AF: 0.737

Gnomad OTH AF: 0.692

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

GnomAD4 genome AF: 0.747 AC: 113404 AN: 151772 Hom.: 42611 Cov.: 30 AF XY: 0.753 AC XY: 55840 AN XY: 74164

African (AFR) AF: 0.774 AC: 32044 AN: 41376

American (AMR) AF: 0.730 AC: 11122 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.594 AC: 2054 AN: 3458

East Asian (EAS) AF: 0.588 AC: 3023 AN: 5144

South Asian (SAS) AF: 0.723 AC: 3467 AN: 4792

European-Finnish (FIN) AF: 0.879 AC: 9272 AN: 10548

Middle Eastern (MID) AF: 0.636 AC: 187 AN: 294

European-Non Finnish (NFE) AF: 0.737 AC: 50035 AN: 67900

Other (OTH) AF: 0.695 AC: 1460 AN: 2102

Alfa AF: 0.723 Hom.: 50281

Bravo AF: 0.734

Asia WGS AF: 0.674 AC: 2342 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	0.15
DANN	Benign	0.64
PhyloP100		-2.1

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: rs180925;

hg19: chr10-115734935;