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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376637	XR_001748194.1	n.58+76049A>G		intron_variant	Intron 1 of 3
LOC105376637	XR_001748195.2	n.58+76049A>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;