rs11603288

Variant names:

• chr11-69229315-G-A
• rs11603288
• NR_188530.1:n.2875C>T

Your query was ambiguous. Multiple possible variants found:

• chr11-69229315-G-A
• chr11-69229315-G-C

Variant summary

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

The NR_188530.1(LOC105369367):​n.2875C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.151 in 152,294 control chromosomes in the GnomAD database, including 2,248 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 0.15 (2248 hom., cov: 33)
• Consequence: LOC105369367 NR_188530.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.678
• Publications: 3 publications found

Genes affected

LOC105369367 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.215 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369367	NR_188530.1	n.2875C>T		non_coding_transcript_exon_variant	Exon 4 of 4
LOC105369367	NR_188531.1	n.2209C>T		non_coding_transcript_exon_variant	Exon 5 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000301530	ENST00000779509.1	n.139-19046G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.151 AC: 22981 AN: 152176 Hom.: 2250 Cov.: 33

Gnomad AFR AF: 0.0417

Gnomad AMI AF: 0.413

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.143

Gnomad EAS AF: 0.0262

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.128

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.218

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.151 AC: 22982 AN: 152294 Hom.: 2248 Cov.: 33 AF XY: 0.145 AC XY: 10772 AN XY: 74468

African (AFR) AF: 0.0416 AC: 1729 AN: 41572

American (AMR) AF: 0.199 AC: 3042 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.143 AC: 497 AN: 3472

East Asian (EAS) AF: 0.0260 AC: 135 AN: 5188

South Asian (SAS) AF: 0.119 AC: 576 AN: 4822

European-Finnish (FIN) AF: 0.128 AC: 1359 AN: 10606

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.218 AC: 14835 AN: 68010

Other (OTH) AF: 0.177 AC: 375 AN: 2114

Alfa AF: 0.198 Hom.: 1949

Bravo AF: 0.154

Asia WGS AF: 0.0730 AC: 255 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.6
DANN	Benign	0.86
PhyloP100		0.68

Splicing

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

Other links and lift over

dbSNP: rs11603288; hg19: chr11-68996782;