rs511512

Variant names:

• chr13-76476277-G-A
• rs511512
• XR_001749919.1:n.157+13414G>A

Variant summary

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

The XR_001749919.1(LOC105370263):​n.157+13414G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.45 in 151,810 control chromosomes in the GnomAD database, including 15,618 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 0.45 (15618 hom., cov: 31)
• Consequence: LOC105370263 XR_001749919.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17
• Publications: 0 publications found

Genes affected

LOC105370263 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.514 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.450 AC: 68334 AN: 151690 Hom.: 15606 Cov.: 31

Gnomad AFR AF: 0.416

Gnomad AMI AF: 0.431

Gnomad AMR AF: 0.341

Gnomad ASJ AF: 0.454

Gnomad EAS AF: 0.530

Gnomad SAS AF: 0.470

Gnomad FIN AF: 0.539

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.476

Gnomad OTH AF: 0.420

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

GnomAD4 genome AF: 0.450 AC: 68388 AN: 151810 Hom.: 15618 Cov.: 31 AF XY: 0.450 AC XY: 33392 AN XY: 74174

African (AFR) AF: 0.416 AC: 17220 AN: 41398

American (AMR) AF: 0.341 AC: 5192 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.454 AC: 1575 AN: 3470

East Asian (EAS) AF: 0.530 AC: 2732 AN: 5150

South Asian (SAS) AF: 0.469 AC: 2262 AN: 4820

European-Finnish (FIN) AF: 0.539 AC: 5684 AN: 10540

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.476 AC: 32336 AN: 67896

Other (OTH) AF: 0.425 AC: 896 AN: 2110

Alfa AF: 0.466 Hom.: 12508

Bravo AF: 0.431

Asia WGS AF: 0.499 AC: 1732 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	1.5
DANN	Benign	0.61
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs511512; hg19: chr13-77050413;