rs12457731

chr18-22611481-G-Achr18-22611481-G-Cchr18-22611481-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The XR_007066307.1(LOC124904262):n.1506+1284C>T variant causes a intron, non coding transcript 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: LOC124904262 XR_007066307.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.65

Genes affected

LOC124904262 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 male gnomad4 subpopulation. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 34 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124904262	XR_007066307.1	n.1506+1284C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.00104

Gnomad4 AMR AF: 0.0481

Gnomad4 ASJ AF: 0.000576

Gnomad4 EAS AF: 0.0361

Gnomad4 SAS AF: 0.00187

Gnomad4 FIN AF: 0.00123

Gnomad4 NFE AF: 0.000470

Gnomad4 OTH AF: 0.00662

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12457731; hg19: chr18-20191444;