rs11232535

Variant names:

• chr11-81217766-T-C
• rs11232535
• ENST00000671134.1:n.323+39837T>C

Your query was ambiguous. Multiple possible variants found:

• chr11-81217766-T-C
• chr11-81217766-T-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000671134.1(ENSG00000287912):​n.323+39837T>C variant causes a intron 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: ENSG00000287912 ENST00000671134.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.283
• Publications: 5 publications found

Genes affected

ENSG00000287912 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287912	ENST00000671134.1	n.323+39837T>C		intron_variant	Intron 2 of 4
ENSG00000287912	ENST00000671210.1	n.309+39837T>C		intron_variant	Intron 2 of 2
ENSG00000287912	ENST00000701193.2	n.195+42450T>C		intron_variant	Intron 1 of 3

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

African (AFR) AF: 0.370 AC: 15352 AN: 41452

American (AMR) AF: 0.0757 AC: 1157 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0628 AC: 218 AN: 3470

East Asian (EAS) AF: 0.0686 AC: 356 AN: 5188

South Asian (SAS) AF: 0.0650 AC: 314 AN: 4828

European-Finnish (FIN) AF: 0.0336 AC: 357 AN: 10616

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.0572 AC: 3890 AN: 68016

Other (OTH) AF: 0.116 AC: 245 AN: 2110

Alfa AF: 0.0915 Hom.: 3677

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
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs11232535; hg19: chr11-80928809;