rs522958

chr12-28075634-G-Achr12-28075634-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_931461.3(LOC105369710):n.156-11747C>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 0.651 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.49

Genes affected

LOC105369710 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC105369710	XR_931461.3	n.156-11747C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.643

Gnomad4 AMR AF: 0.587

Gnomad4 ASJ AF: 0.617

Gnomad4 EAS AF: 0.697

Gnomad4 SAS AF: 0.614

Gnomad4 FIN AF: 0.645

Gnomad4 NFE AF: 0.671

Gnomad4 OTH AF: 0.655

Alfa AF: 0.669 Hom.: 42555

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs522958; hg19: chr12-28228567;