11-746992-T-G

Variant names:

• chr11-746992-T-G
• rs10794338
• XR_930962.3:n.*30T>G

Variant summary

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

The XR_930962.3(LOC105376509):​n.*30T>G variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.281 in 152,054 control chromosomes in the GnomAD database, including 7,601 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 0.28 (7601 hom., cov: 34)
• Consequence: LOC105376509 XR_930962.3 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.300
• Publications: 4 publications found

Genes affected

LOC105376509 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.503 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: 0.281 AC: 42669 AN: 151934 Hom.: 7588 Cov.: 34

Gnomad AFR AF: 0.509

Gnomad AMI AF: 0.141

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.143

Gnomad EAS AF: 0.0952

Gnomad SAS AF: 0.125

Gnomad FIN AF: 0.195

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.212

Gnomad OTH AF: 0.247

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

GnomAD4 genome AF: 0.281 AC: 42715 AN: 152054 Hom.: 7601 Cov.: 34 AF XY: 0.275 AC XY: 20436 AN XY: 74336

African (AFR) AF: 0.509 AC: 21133 AN: 41540

American (AMR) AF: 0.188 AC: 2879 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.143 AC: 496 AN: 3470

East Asian (EAS) AF: 0.0954 AC: 487 AN: 5106

South Asian (SAS) AF: 0.123 AC: 590 AN: 4798

European-Finnish (FIN) AF: 0.195 AC: 2064 AN: 10600

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.212 AC: 14378 AN: 67934

Other (OTH) AF: 0.251 AC: 530 AN: 2114

Alfa AF: 0.108 Hom.: 1831

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.2
DANN	Benign	0.16
PhyloP100		-0.30
PromoterAI		0.033	Neutral

Splicing

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

Other links and lift over

dbSNP: rs10794338; hg19: chr11-746992;