rs12457731

Variant names:

• chr18-22611481-G-A
• rs12457731
• ENST00000716263.1:n.817+1284C>T

Your query was ambiguous. Multiple possible variants found:

• chr18-22611481-G-A
• chr18-22611481-G-C
• chr18-22611481-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000716263.1(ENSG00000266850):​n.817+1284C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0068 in 152,252 control chromosomes in the GnomAD database, including 34 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 0.0068 (34 hom., cov: 32)
• Consequence: ENSG00000266850 ENST00000716263.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.65
• Publications: 2 publications found

Genes affected

ENSG00000266850 (HGNC:58091):

LOC124904262 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BS1: Variant frequency is greater than expected in population amr. GnomAd4 allele frequency = 0.0068 (1036/152252) while in subpopulation AMR AF = 0.0481 (736/15292). AF 95% confidence interval is 0.0452. There are 34 homozygotes in GnomAd4. There are 575 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 34 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124904262	XR_007066307.1	n.1506+1284C>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000266850	ENST00000716263.1	n.817+1284C>T		intron_variant	Intron 6 of 6
ENSG00000266850	ENST00000716264.1	n.1012+1284C>T		intron_variant	Intron 8 of 8
ENSG00000266850	ENST00000795021.1	n.678-1288C>T		intron_variant	Intron 5 of 5

Frequencies

GnomAD3 genomes AF: 0.00681 AC: 1036 AN: 152134 Hom.: 34 Cov.: 32

Gnomad AFR AF: 0.00104

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0481

Gnomad ASJ AF: 0.000576

Gnomad EAS AF: 0.0362

Gnomad SAS AF: 0.00207

Gnomad FIN AF: 0.00123

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000456

Gnomad OTH AF: 0.00716

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

GnomAD4 genome AF: 0.00680 AC: 1036 AN: 152252 Hom.: 34 Cov.: 32 AF XY: 0.00772 AC XY: 575 AN XY: 74442

African (AFR) AF: 0.00104 AC: 43 AN: 41538

American (AMR) AF: 0.0481 AC: 736 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.000576 AC: 2 AN: 3472

East Asian (EAS) AF: 0.0361 AC: 187 AN: 5178

South Asian (SAS) AF: 0.00187 AC: 9 AN: 4824

European-Finnish (FIN) AF: 0.00123 AC: 13 AN: 10608

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.000470 AC: 32 AN: 68018

Other (OTH) AF: 0.00662 AC: 14 AN: 2116

Alfa AF: 0.00809 Hom.: 7

Bravo AF: 0.0104

Asia WGS AF: 0.0170 AC: 59 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	8.6
DANN	Benign	0.66
PhyloP100		1.6

Splicing

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

Other links and lift over

dbSNP: rs12457731; hg19: chr18-20191444;