rs12040131

Variant names:

• chr1-22663205-C-G
• rs12040131
• ENST00000836788.1:n.50G>C

Variant summary

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

The ENST00000836788.1(ENSG00000308848):​n.50G>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.162 in 152,234 control chromosomes in the GnomAD database, including 2,485 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 0.16 (2485 hom., cov: 32)
• Consequence: ENSG00000308848 ENST00000836788.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.114
• Publications: 4 publications found

Genes affected

ENSG00000308848 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.222 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
ENSG00000308848	ENST00000836788.1	n.50G>C		non_coding_transcript_exon_variant	Exon 1 of 2

Frequencies

GnomAD3 genomes AF: 0.162 AC: 24716 AN: 152116 Hom.: 2487 Cov.: 32

Gnomad AFR AF: 0.0511

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.229

Gnomad ASJ AF: 0.155

Gnomad EAS AF: 0.0250

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.195

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.225

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.162 AC: 24713 AN: 152234 Hom.: 2485 Cov.: 32 AF XY: 0.161 AC XY: 11991 AN XY: 74434

African (AFR) AF: 0.0509 AC: 2117 AN: 41560

American (AMR) AF: 0.228 AC: 3492 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.155 AC: 538 AN: 3470

East Asian (EAS) AF: 0.0251 AC: 130 AN: 5180

South Asian (SAS) AF: 0.119 AC: 575 AN: 4824

European-Finnish (FIN) AF: 0.195 AC: 2067 AN: 10602

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.224 AC: 15264 AN: 67992

Other (OTH) AF: 0.180 AC: 380 AN: 2112

Alfa AF: 0.188 Hom.: 421

Bravo AF: 0.163

Asia WGS AF: 0.0840 AC: 293 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.4
DANN	Benign	0.66
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs12040131; hg19: chr1-22989698;