rs10880174

Variant names:

• chr12-41860271-C-A
• rs10880174
• ENST00000550874.1:n.472-30346G>T

Your query was ambiguous. Multiple possible variants found:

• chr12-41860271-C-A
• chr12-41860271-C-T

Variant summary

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

The ENST00000550874.1(ENSG00000257239):​n.472-30346G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.141 in 152,200 control chromosomes in the GnomAD database, including 1,513 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 0.14 (1513 hom., cov: 32)
• Consequence: ENSG00000257239 ENST00000550874.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.486
• Publications: 1 publications found

Genes affected

ENSG00000257239 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.164 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000550874.1. 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
	ENSG00000257239	ENST00000550874.1	TSL:3	n.472-30346G>T		intron	N/A
	ENSG00000257239	ENST00000824751.1		n.123-30346G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.141 AC: 21503 AN: 152080 Hom.: 1511 Cov.: 32

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.136

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.175

Gnomad FIN AF: 0.127

Gnomad MID AF: 0.153

Gnomad NFE AF: 0.141

Gnomad OTH AF: 0.135

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

GnomAD4 genome AF: 0.141 AC: 21506 AN: 152200 Hom.: 1513 Cov.: 32 AF XY: 0.142 AC XY: 10586 AN XY: 74398

African (AFR) AF: 0.140 AC: 5799 AN: 41532

American (AMR) AF: 0.140 AC: 2138 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.129 AC: 449 AN: 3470

East Asian (EAS) AF: 0.172 AC: 889 AN: 5172

South Asian (SAS) AF: 0.174 AC: 840 AN: 4824

European-Finnish (FIN) AF: 0.127 AC: 1349 AN: 10600

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.141 AC: 9594 AN: 68004

Other (OTH) AF: 0.133 AC: 280 AN: 2108

Alfa AF: 0.136 Hom.: 2447

Bravo AF: 0.141

Asia WGS AF: 0.148 AC: 514 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	8.7
DANN	Benign	0.50
PhyloP100		0.49

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: rs10880174;

hg19: chr12-42254073;