chr11-34538699-G-C

Variant names:

• chr11-34538699-G-C
• rs836126
• ENST00000527984.1:n.237-5533C>G

Variant summary

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

The ENST00000527984.1(ENSG00000255271):​n.237-5533C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.172 in 152,086 control chromosomes in the GnomAD database, including 2,878 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 0.17 (2878 hom., cov: 31)
• Consequence: ENSG00000255271 ENST00000527984.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.937
• Publications: 1 publications found

Genes affected

ENSG00000255271 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 = 0.387 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
ENSG00000255271	ENST00000527984.1	n.237-5533C>G		intron_variant	Intron 2 of 2	2
ENSG00000301952	ENST00000783043.1	n.315+2420G>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.171 AC: 26046 AN: 151968 Hom.: 2854 Cov.: 31

Gnomad AFR AF: 0.289

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.147

Gnomad ASJ AF: 0.0957

Gnomad EAS AF: 0.401

Gnomad SAS AF: 0.0896

Gnomad FIN AF: 0.0520

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.173

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

GnomAD4 genome AF: 0.172 AC: 26119 AN: 152086 Hom.: 2878 Cov.: 31 AF XY: 0.169 AC XY: 12571 AN XY: 74366

African (AFR) AF: 0.290 AC: 12028 AN: 41454

American (AMR) AF: 0.147 AC: 2239 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0957 AC: 332 AN: 3470

East Asian (EAS) AF: 0.402 AC: 2078 AN: 5174

South Asian (SAS) AF: 0.0895 AC: 432 AN: 4828

European-Finnish (FIN) AF: 0.0520 AC: 551 AN: 10594

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.117 AC: 7960 AN: 67970

Other (OTH) AF: 0.178 AC: 375 AN: 2110

Alfa AF: 0.0442 Hom.: 39

Bravo AF: 0.189

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.11
DANN	Benign	0.67
PhyloP100		-0.94

Splicing

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

Other links and lift over

dbSNP: rs836126; hg19: chr11-34560246;