11-746992-T-C

Position:

• chr11-746992-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The 11-746992-T-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

Genes affected

LOC105376509 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105376509	XR_930962.3			downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.351

Gnomad4 AMR AF: 0.442

Gnomad4 ASJ AF: 0.371

Gnomad4 EAS AF: 0.489

Gnomad4 SAS AF: 0.351

Gnomad4 FIN AF: 0.510

Gnomad4 NFE AF: 0.499

Gnomad4 OTH AF: 0.435

Alfa AF: 0.573 Hom.: 1831

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.8
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10794338; hg19: chr11-746992;