11-92968430-T-C

Variant names:

• chr11-92968430-T-C
• rs4753426
• XR_007062838.1:n.2193T>C

Variant summary

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

The XR_007062838.1(LOC124902733):​n.2193T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.499 in 152,010 control chromosomes in the GnomAD database, including 19,426 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 0.50 (19426 hom., cov: 32)
• Consequence: LOC124902733 XR_007062838.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.123
• Publications: 65 publications found

Genes affected

LOC124902733 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.681 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: 0.499 AC: 75737 AN: 151892 Hom.: 19413 Cov.: 32

Gnomad AFR AF: 0.430

Gnomad AMI AF: 0.678

Gnomad AMR AF: 0.624

Gnomad ASJ AF: 0.419

Gnomad EAS AF: 0.700

Gnomad SAS AF: 0.590

Gnomad FIN AF: 0.570

Gnomad MID AF: 0.490

Gnomad NFE AF: 0.481

Gnomad OTH AF: 0.495

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

GnomAD4 genome AF: 0.499 AC: 75793 AN: 152010 Hom.: 19426 Cov.: 32 AF XY: 0.508 AC XY: 37739 AN XY: 74290

African (AFR) AF: 0.430 AC: 17838 AN: 41466

American (AMR) AF: 0.625 AC: 9552 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.419 AC: 1454 AN: 3470

East Asian (EAS) AF: 0.700 AC: 3621 AN: 5170

South Asian (SAS) AF: 0.590 AC: 2843 AN: 4818

European-Finnish (FIN) AF: 0.570 AC: 6012 AN: 10550

Middle Eastern (MID) AF: 0.493 AC: 144 AN: 292

European-Non Finnish (NFE) AF: 0.481 AC: 32665 AN: 67942

Other (OTH) AF: 0.496 AC: 1046 AN: 2110

Alfa AF: 0.489 Hom.: 22233

Bravo AF: 0.501

Asia WGS AF: 0.588 AC: 2043 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.4
DANN	Benign	0.84
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs4753426; hg19: chr11-92701596;