rs11213703

Positions:

• chr11-111019216-T-C

Variant summary

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

The ENST00000660486.1(ENSG00000287556):​n.50+5715T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.377 in 152,090 control chromosomes in the GnomAD database, including 11,528 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 (11528 hom., cov: 33)
• Consequence: ENST00000660486.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0490

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• 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.1278-558A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000660486.1	n.50+5715T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.377 AC: 57241 AN: 151972 Hom.: 11512 Cov.: 33

Gnomad AFR AF: 0.391

Gnomad AMI AF: 0.262

Gnomad AMR AF: 0.394

Gnomad ASJ AF: 0.434

Gnomad EAS AF: 0.788

Gnomad SAS AF: 0.658

Gnomad FIN AF: 0.327

Gnomad MID AF: 0.471

Gnomad NFE AF: 0.318

Gnomad OTH AF: 0.382

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

GnomAD4 genome AF: 0.377 AC: 57297 AN: 152090 Hom.: 11528 Cov.: 33 AF XY: 0.387 AC XY: 28755 AN XY: 74338

Gnomad4 AFR AF: 0.391

Gnomad4 AMR AF: 0.395

Gnomad4 ASJ AF: 0.434

Gnomad4 EAS AF: 0.787

Gnomad4 SAS AF: 0.658

Gnomad4 FIN AF: 0.327

Gnomad4 NFE AF: 0.318

Gnomad4 OTH AF: 0.388

Alfa AF: 0.352 Hom.: 5261

Bravo AF: 0.380

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	-0.96
CADD	Benign	5.2
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11213703; hg19: chr11-110889940;