11-24312511-G-T

Variant names:

• chr11-24312511-G-T
• rs731365
• XR_931131.1:n.147+1267C>A

Variant summary

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

The XR_931131.1(LOC105376595):​n.147+1267C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.426 in 151,948 control chromosomes in the GnomAD database, including 14,002 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 0.43 (14002 hom., cov: 32)
• Consequence: LOC105376595 XR_931131.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.152
• Publications: 4 publications found

Genes affected

LOC105376595 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.431 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.427 AC: 64761 AN: 151830 Hom.: 13987 Cov.: 32

Gnomad AFR AF: 0.436

Gnomad AMI AF: 0.482

Gnomad AMR AF: 0.381

Gnomad ASJ AF: 0.411

Gnomad EAS AF: 0.374

Gnomad SAS AF: 0.373

Gnomad FIN AF: 0.487

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.429

Gnomad OTH AF: 0.446

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

GnomAD4 genome AF: 0.426 AC: 64805 AN: 151948 Hom.: 14002 Cov.: 32 AF XY: 0.427 AC XY: 31668 AN XY: 74250

African (AFR) AF: 0.436 AC: 18060 AN: 41434

American (AMR) AF: 0.381 AC: 5813 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.411 AC: 1424 AN: 3464

East Asian (EAS) AF: 0.375 AC: 1937 AN: 5160

South Asian (SAS) AF: 0.373 AC: 1797 AN: 4816

European-Finnish (FIN) AF: 0.487 AC: 5140 AN: 10558

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.429 AC: 29116 AN: 67948

Other (OTH) AF: 0.446 AC: 938 AN: 2104

Alfa AF: 0.426 Hom.: 3636

Bravo AF: 0.419

Asia WGS AF: 0.351 AC: 1220 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.66
DANN	Benign	0.54
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs731365; hg19: chr11-24334057;