11-113493925-G-T

Variant names:

• chr11-113493925-G-T
• rs4245150
• XR_948024.2:n.107-2735C>A

Variant summary

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

The XR_948024.2(LOC105369501):​n.107-2735C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.719 in 151,994 control chromosomes in the GnomAD database, including 40,019 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 0.72 (40019 hom., cov: 31)
• Consequence: LOC105369501 XR_948024.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.317
• Publications: 16 publications found

Genes affected

LOC105369501 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.952 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.718 AC: 109114 AN: 151876 Hom.: 39957 Cov.: 31

Gnomad AFR AF: 0.824

Gnomad AMI AF: 0.736

Gnomad AMR AF: 0.682

Gnomad ASJ AF: 0.565

Gnomad EAS AF: 0.974

Gnomad SAS AF: 0.756

Gnomad FIN AF: 0.822

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.635

Gnomad OTH AF: 0.653

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

GnomAD4 genome AF: 0.719 AC: 109239 AN: 151994 Hom.: 40019 Cov.: 31 AF XY: 0.729 AC XY: 54168 AN XY: 74296

African (AFR) AF: 0.824 AC: 34168 AN: 41466

American (AMR) AF: 0.682 AC: 10415 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.565 AC: 1959 AN: 3468

East Asian (EAS) AF: 0.974 AC: 5028 AN: 5162

South Asian (SAS) AF: 0.757 AC: 3634 AN: 4802

European-Finnish (FIN) AF: 0.822 AC: 8683 AN: 10558

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.634 AC: 43122 AN: 67964

Other (OTH) AF: 0.657 AC: 1384 AN: 2106

Alfa AF: 0.666 Hom.: 56606

Bravo AF: 0.709

Asia WGS AF: 0.867 AC: 3012 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.6
DANN	Benign	0.49
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs4245150; hg19: chr11-113364647;