rs12042640

Variant names:

• chr1-62901125-T-C
• rs12042640
• ENST00000450811.1:n.102-169T>C

Variant summary

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

The ENST00000450811.1(ENSG00000234318):​n.102-169T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.626 in 151,500 control chromosomes in the GnomAD database, including 32,618 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 0.63 (32618 hom., cov: 29)
• Consequence: ENSG00000234318 ENST00000450811.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0960
• Publications: 4 publications found

Genes affected

ENSG00000234318 (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 (EAS) allele frequency at 95% confidence interval = 0.945 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
ENSG00000234318	ENST00000450811.1	n.102-169T>C		intron_variant	Intron 1 of 1	3
ENSG00000306496	ENST00000819120.1	n.309+4908A>G		intron_variant	Intron 2 of 3
ENSG00000306496	ENST00000819121.1	n.219+4962A>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.627 AC: 94861 AN: 151386 Hom.: 32617 Cov.: 29

Gnomad AFR AF: 0.317

Gnomad AMI AF: 0.804

Gnomad AMR AF: 0.741

Gnomad ASJ AF: 0.709

Gnomad EAS AF: 0.967

Gnomad SAS AF: 0.753

Gnomad FIN AF: 0.775

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.724

Gnomad OTH AF: 0.655

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

GnomAD4 genome AF: 0.626 AC: 94889 AN: 151500 Hom.: 32618 Cov.: 29 AF XY: 0.633 AC XY: 46829 AN XY: 73928

African (AFR) AF: 0.316 AC: 13079 AN: 41334

American (AMR) AF: 0.741 AC: 11271 AN: 15208

Ashkenazi Jewish (ASJ) AF: 0.709 AC: 2459 AN: 3470

East Asian (EAS) AF: 0.967 AC: 4972 AN: 5140

South Asian (SAS) AF: 0.752 AC: 3594 AN: 4778

European-Finnish (FIN) AF: 0.775 AC: 8025 AN: 10358

Middle Eastern (MID) AF: 0.728 AC: 214 AN: 294

European-Non Finnish (NFE) AF: 0.724 AC: 49163 AN: 67912

Other (OTH) AF: 0.659 AC: 1384 AN: 2100

Alfa AF: 0.680 Hom.: 7372

Bravo AF: 0.611

Asia WGS AF: 0.835 AC: 2899 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.8
DANN	Benign	0.56
PhyloP100		-0.096

Splicing

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

Other links and lift over

dbSNP: rs12042640; hg19: chr1-63366796;