rs12665174

Variant names:

• chr6-25044580-C-G
• rs12665174
• ENST00000428903.1:n.78+2664C>G

Variant summary

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

The ENST00000428903.1(ENSG00000229313):​n.78+2664C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.178 in 151,890 control chromosomes in the GnomAD database, including 2,800 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 0.18 (2800 hom., cov: 31)
• Consequence: ENSG00000229313 ENST00000428903.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.94
• Publications: 1 publications found

Genes affected

ENSG00000229313 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.253 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000229313	ENST00000428903.1	n.78+2664C>G		intron_variant	Intron 1 of 2	5
ENSG00000288887	ENST00000761912.1	n.734+19808C>G		intron_variant	Intron 1 of 2
ENSG00000285801	ENST00000762009.1	n.827+19566C>G		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.178 AC: 27071 AN: 151772 Hom.: 2800 Cov.: 31

Gnomad AFR AF: 0.0789

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.227

Gnomad ASJ AF: 0.141

Gnomad EAS AF: 0.265

Gnomad SAS AF: 0.165

Gnomad FIN AF: 0.183

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.224

Gnomad OTH AF: 0.171

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

GnomAD4 genome AF: 0.178 AC: 27074 AN: 151890 Hom.: 2800 Cov.: 31 AF XY: 0.175 AC XY: 12992 AN XY: 74198

African (AFR) AF: 0.0789 AC: 3269 AN: 41424

American (AMR) AF: 0.228 AC: 3469 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.141 AC: 491 AN: 3472

East Asian (EAS) AF: 0.265 AC: 1366 AN: 5160

South Asian (SAS) AF: 0.165 AC: 796 AN: 4816

European-Finnish (FIN) AF: 0.183 AC: 1920 AN: 10512

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.224 AC: 15217 AN: 67962

Other (OTH) AF: 0.171 AC: 361 AN: 2106

Alfa AF: 0.197 Hom.: 407

Bravo AF: 0.179

Asia WGS AF: 0.210 AC: 734 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.086
DANN	Benign	0.68
PhyloP100		-3.9
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs12665174; hg19: chr6-25044808;