11-6735165-T-C

Variant names:

• chr11-6735165-T-C
• rs951340
• ENST00000526769.3:n.91+11184A>G

Variant summary

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

The ENST00000526769.3(ENSG00000291143):​n.91+11184A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.364 in 151,996 control chromosomes in the GnomAD database, including 11,302 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 0.36 (11302 hom., cov: 32)
• Consequence: ENSG00000291143 ENST00000526769.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.408

Genes affected

ENSG00000291143 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.441 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
ENSG00000291143	ENST00000526769.3	n.91+11184A>G		intron_variant	Intron 1 of 1	1
ENSG00000291143	ENST00000687034.2	n.149-1016A>G		intron_variant	Intron 1 of 1
ENSG00000291143	ENST00000702834.1	n.127-998A>G		intron_variant	Intron 1 of 1
ENSG00000291143	ENST00000702907.1	n.94-1024A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.365 AC: 55369 AN: 151878 Hom.: 11303 Cov.: 32

Gnomad AFR AF: 0.179

Gnomad AMI AF: 0.519

Gnomad AMR AF: 0.348

Gnomad ASJ AF: 0.413

Gnomad EAS AF: 0.449

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.544

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.445

Gnomad OTH AF: 0.380

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

GnomAD4 genome AF: 0.364 AC: 55388 AN: 151996 Hom.: 11302 Cov.: 32 AF XY: 0.368 AC XY: 27364 AN XY: 74290

Gnomad4 AFR AF: 0.180

Gnomad4 AMR AF: 0.347

Gnomad4 ASJ AF: 0.413

Gnomad4 EAS AF: 0.449

Gnomad4 SAS AF: 0.314

Gnomad4 FIN AF: 0.544

Gnomad4 NFE AF: 0.445

Gnomad4 OTH AF: 0.376

Alfa AF: 0.406 Hom.: 6815

Bravo AF: 0.342

Asia WGS AF: 0.333 AC: 1158 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.5
DANN	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs951340; hg19: chr11-6756396;