rs12131057

Variant names:

• chr1-38158457-G-A
• rs12131057
• ENST00000655033.1:n.636-3236G>A

Variant summary

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

The ENST00000655033.1(ENSG00000286552):​n.636-3236G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.198 in 151,998 control chromosomes in the GnomAD database, including 3,337 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 0.20 (3337 hom., cov: 31)
• Consequence: ENSG00000286552 ENST00000655033.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.344
• Publications: 21 publications found

Genes affected

ENSG00000286552 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.246 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378654	XR_001737985.1	n.61+16743G>A		intron_variant	Intron 1 of 4
LOC105378654	XR_001737986.1	n.45-3236G>A		intron_variant	Intron 1 of 4
LOC105378654	XR_001737987.2	n.45-3236G>A		intron_variant	Intron 1 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286552	ENST00000655033.1	n.636-3236G>A		intron_variant	Intron 1 of 2
ENSG00000286552	ENST00000810720.1	n.73-3236G>A		intron_variant	Intron 1 of 2
ENSG00000286552	ENST00000810721.1	n.143-3236G>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.198 AC: 30086 AN: 151880 Hom.: 3334 Cov.: 31

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.454

Gnomad AMR AF: 0.156

Gnomad ASJ AF: 0.261

Gnomad EAS AF: 0.0124

Gnomad SAS AF: 0.194

Gnomad FIN AF: 0.259

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.249

Gnomad OTH AF: 0.213

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

GnomAD4 genome AF: 0.198 AC: 30102 AN: 151998 Hom.: 3337 Cov.: 31 AF XY: 0.198 AC XY: 14686 AN XY: 74304

African (AFR) AF: 0.126 AC: 5242 AN: 41456

American (AMR) AF: 0.156 AC: 2380 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.261 AC: 905 AN: 3470

East Asian (EAS) AF: 0.0120 AC: 62 AN: 5168

South Asian (SAS) AF: 0.195 AC: 939 AN: 4816

European-Finnish (FIN) AF: 0.259 AC: 2729 AN: 10552

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.249 AC: 16912 AN: 67938

Other (OTH) AF: 0.218 AC: 461 AN: 2114

Alfa AF: 0.224 Hom.: 13000

Bravo AF: 0.183

Asia WGS AF: 0.120 AC: 417 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.6
DANN	Benign	0.78
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs12131057; hg19: chr1-38624129;