rs11232535

chr11-81217766-T-Cchr11-81217766-T-G

Variant summary

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

The ENST00000701193.1(ENSG00000287912):n.113+42450T>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 0.144 in 152,172 control chromosomes in the GnomAD database, including 3,054 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 0.14 (3054 hom., cov: 32)
• Consequence: ENST00000701193.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.283

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.365 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000701193.1	n.113+42450T>C		intron_variant, non_coding_transcript_variant
	ENST00000671134.1	n.323+39837T>C		intron_variant, non_coding_transcript_variant
	ENST00000671210.1	n.309+39837T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.144 AC: 21882 AN: 152054 Hom.: 3046 Cov.: 32

Gnomad AFR AF: 0.370

Gnomad AMI AF: 0.00768

Gnomad AMR AF: 0.0759

Gnomad ASJ AF: 0.0628

Gnomad EAS AF: 0.0685

Gnomad SAS AF: 0.0652

Gnomad FIN AF: 0.0336

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.0572

Gnomad OTH AF: 0.117

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

GnomAD4 genome AF: 0.144 AC: 21928 AN: 152172 Hom.: 3054 Cov.: 32 AF XY: 0.141 AC XY: 10511 AN XY: 74432

Gnomad4 AFR AF: 0.370

Gnomad4 AMR AF: 0.0757

Gnomad4 ASJ AF: 0.0628

Gnomad4 EAS AF: 0.0686

Gnomad4 SAS AF: 0.0650

Gnomad4 FIN AF: 0.0336

Gnomad4 NFE AF: 0.0572

Gnomad4 OTH AF: 0.116

Alfa AF: 0.0695 Hom.: 731

Bravo AF: 0.158

Asia WGS AF: 0.0780 AC: 272 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	6.3
Dann	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11232535; hg19: chr11-80928809;