11-746992-T-C

Variant names:

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

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>C variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.446 in 152,034 control chromosomes in the GnomAD database, including 15,406 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 (15406 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 (NFE) allele frequency at 95% confidence interval = 0.494 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: 0.446 AC: 67685 AN: 151914 Hom.: 15388 Cov.: 34

Gnomad AFR AF: 0.351

Gnomad AMI AF: 0.654

Gnomad AMR AF: 0.442

Gnomad ASJ AF: 0.371

Gnomad EAS AF: 0.490

Gnomad SAS AF: 0.350

Gnomad FIN AF: 0.510

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.499

Gnomad OTH AF: 0.434

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

GnomAD4 genome AF: 0.446 AC: 67753 AN: 152034 Hom.: 15406 Cov.: 34 AF XY: 0.444 AC XY: 32977 AN XY: 74330

African (AFR) AF: 0.351 AC: 14580 AN: 41522

American (AMR) AF: 0.442 AC: 6758 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.371 AC: 1287 AN: 3470

East Asian (EAS) AF: 0.489 AC: 2498 AN: 5104

South Asian (SAS) AF: 0.351 AC: 1687 AN: 4800

European-Finnish (FIN) AF: 0.510 AC: 5403 AN: 10598

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.499 AC: 33892 AN: 67938

Other (OTH) AF: 0.435 AC: 918 AN: 2112

Alfa AF: 0.573 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	1.8
DANN	Benign	0.33
PhyloP100		-0.30
PromoterAI		0.020	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;