rs522958

Variant names:

• chr12-28075634-G-A
• rs522958
• XR_931461.3:n.156-11747C>T

Your query was ambiguous. Multiple possible variants found:

• chr12-28075634-G-A
• chr12-28075634-G-C
• chr12-28075634-G-T

Variant summary

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

The XR_931461.3(LOC105369710):​n.156-11747C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.651 in 152,056 control chromosomes in the GnomAD database, including 32,445 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 0.65 (32445 hom., cov: 32)
• Consequence: LOC105369710 XR_931461.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.49
• Publications: 12 publications found

Genes affected

LOC105369710 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.678 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369710	XR_931461.3	n.156-11747C>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.651 AC: 98941 AN: 151938 Hom.: 32427 Cov.: 32

Gnomad AFR AF: 0.643

Gnomad AMI AF: 0.691

Gnomad AMR AF: 0.588

Gnomad ASJ AF: 0.617

Gnomad EAS AF: 0.698

Gnomad SAS AF: 0.615

Gnomad FIN AF: 0.645

Gnomad MID AF: 0.701

Gnomad NFE AF: 0.671

Gnomad OTH AF: 0.651

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

GnomAD4 genome AF: 0.651 AC: 99000 AN: 152056 Hom.: 32445 Cov.: 32 AF XY: 0.648 AC XY: 48165 AN XY: 74318

African (AFR) AF: 0.643 AC: 26686 AN: 41476

American (AMR) AF: 0.587 AC: 8956 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.617 AC: 2140 AN: 3470

East Asian (EAS) AF: 0.697 AC: 3614 AN: 5184

South Asian (SAS) AF: 0.614 AC: 2960 AN: 4820

European-Finnish (FIN) AF: 0.645 AC: 6810 AN: 10558

Middle Eastern (MID) AF: 0.692 AC: 202 AN: 292

European-Non Finnish (NFE) AF: 0.671 AC: 45622 AN: 67982

Other (OTH) AF: 0.655 AC: 1380 AN: 2108

Alfa AF: 0.667 Hom.: 104242

Bravo AF: 0.652

Asia WGS AF: 0.693 AC: 2412 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.029
DANN	Benign	0.54
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs522958; hg19: chr12-28228567;