rs11035577

Variant names:

• chr11-39887112-T-C
• rs11035577
• XR_001748194.1:n.58+76049A>G

Variant summary

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

The XR_001748194.1(LOC105376637):​n.58+76049A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.102 in 151,720 control chromosomes in the GnomAD database, including 999 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 0.10 (999 hom., cov: 31)
• Consequence: LOC105376637 XR_001748194.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.462
• Publications: 2 publications found

Genes affected

LOC105376637 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.143 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.102 AC: 15513 AN: 151614 Hom.: 996 Cov.: 31

Gnomad AFR AF: 0.0456

Gnomad AMI AF: 0.171

Gnomad AMR AF: 0.100

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.0549

Gnomad FIN AF: 0.0828

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.145

Gnomad OTH AF: 0.141

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

GnomAD4 genome AF: 0.102 AC: 15521 AN: 151720 Hom.: 999 Cov.: 31 AF XY: 0.0994 AC XY: 7373 AN XY: 74140

African (AFR) AF: 0.0455 AC: 1887 AN: 41440

American (AMR) AF: 0.100 AC: 1523 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.178 AC: 617 AN: 3470

East Asian (EAS) AF: 0.00155 AC: 8 AN: 5166

South Asian (SAS) AF: 0.0554 AC: 265 AN: 4782

European-Finnish (FIN) AF: 0.0828 AC: 863 AN: 10426

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.145 AC: 9841 AN: 67908

Other (OTH) AF: 0.142 AC: 299 AN: 2110

Alfa AF: 0.128 Hom.: 2743

Bravo AF: 0.103

Asia WGS AF: 0.0480 AC: 168 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.26
DANN	Benign	0.74
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs11035577; hg19: chr11-39908662;