11-111017760-C-T

Position:

• chr11-111017760-C-T

Variant summary

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

The ENST00000660486.1(ENSG00000287556):​n.50+4259C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.376 in 151,998 control chromosomes in the GnomAD database, including 11,475 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 0.38 (11475 hom., cov: 32)
• Consequence: ENSG00000287556 ENST00000660486.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0940

Genes affected

ENSG00000287556 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 = 0.767 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105369489	XR_948009.2	n.1464+712G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000287556	ENST00000660486.1	n.50+4259C>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.376 AC: 57108 AN: 151880 Hom.: 11459 Cov.: 32

Gnomad AFR AF: 0.391

Gnomad AMI AF: 0.261

Gnomad AMR AF: 0.394

Gnomad ASJ AF: 0.416

Gnomad EAS AF: 0.787

Gnomad SAS AF: 0.658

Gnomad FIN AF: 0.326

Gnomad MID AF: 0.471

Gnomad NFE AF: 0.318

Gnomad OTH AF: 0.380

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

GnomAD4 genome AF: 0.376 AC: 57165 AN: 151998 Hom.: 11475 Cov.: 32 AF XY: 0.386 AC XY: 28671 AN XY: 74270

Gnomad4 AFR AF: 0.391

Gnomad4 AMR AF: 0.394

Gnomad4 ASJ AF: 0.416

Gnomad4 EAS AF: 0.787

Gnomad4 SAS AF: 0.658

Gnomad4 FIN AF: 0.326

Gnomad4 NFE AF: 0.318

Gnomad4 OTH AF: 0.386

Alfa AF: 0.343 Hom.: 19227

Bravo AF: 0.379

Asia WGS AF: 0.690 AC: 2397 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.2
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs978769; hg19: chr11-110888484;