rs12408810

Variant names:

• chr1-106098321-C-T
• rs12408810
• ENST00000634868.1:n.463-25455C>T

Variant summary

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

The ENST00000634868.1(ENSG00000237480):​n.463-25455C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.187 in 151,998 control chromosomes in the GnomAD database, including 3,010 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 0.19 (3010 hom., cov: 32)
• Consequence: ENSG00000237480 ENST00000634868.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0220
• Publications: 6 publications found

Genes affected

ENSG00000237480 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.399 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
ENSG00000237480	ENST00000634868.1	n.463-25455C>T		intron_variant	Intron 5 of 5	5

Frequencies

GnomAD3 genomes AF: 0.186 AC: 28306 AN: 151880 Hom.: 2996 Cov.: 32

Gnomad AFR AF: 0.246

Gnomad AMI AF: 0.113

Gnomad AMR AF: 0.226

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.413

Gnomad SAS AF: 0.180

Gnomad FIN AF: 0.127

Gnomad MID AF: 0.229

Gnomad NFE AF: 0.136

Gnomad OTH AF: 0.168

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

GnomAD4 genome AF: 0.187 AC: 28367 AN: 151998 Hom.: 3010 Cov.: 32 AF XY: 0.189 AC XY: 14009 AN XY: 74296

African (AFR) AF: 0.247 AC: 10230 AN: 41456

American (AMR) AF: 0.226 AC: 3457 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.163 AC: 567 AN: 3470

East Asian (EAS) AF: 0.413 AC: 2130 AN: 5152

South Asian (SAS) AF: 0.181 AC: 870 AN: 4814

European-Finnish (FIN) AF: 0.127 AC: 1339 AN: 10576

Middle Eastern (MID) AF: 0.226 AC: 66 AN: 292

European-Non Finnish (NFE) AF: 0.136 AC: 9252 AN: 67950

Other (OTH) AF: 0.167 AC: 353 AN: 2110

Alfa AF: 0.165 Hom.: 3419

Bravo AF: 0.201

Asia WGS AF: 0.262 AC: 907 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.6
DANN	Benign	0.17
PhyloP100		0.022

Splicing

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

Other links and lift over

dbSNP: rs12408810; hg19: chr1-106640943;