rs11228580

Positions:

• chr11-69234875-T-C

Variant summary

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

The XR_007062756.1(LOC105369367):​n.54+6A>G variant causes a splice donor region, intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.149 in 152,074 control chromosomes in the GnomAD database, including 1,817 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 (1817 hom., cov: 31)
• Consequence: LOC105369367 XR_007062756.1 splice_donor_region, intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.283

Genes affected

LOC105369367 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.165 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105369367	XR_007062756.1	n.54+6A>G		splice_donor_region_variant, intron_variant, non_coding_transcript_variant
LOC105369367	XR_007062755.1	n.54+6A>G		splice_donor_region_variant, intron_variant, non_coding_transcript_variant
LOC105369367	XR_007062758.1	n.54+6A>G		splice_donor_region_variant, intron_variant, non_coding_transcript_variant
LOC105369367	XR_950259.2	n.54+6A>G		splice_donor_region_variant, intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.149 AC: 22690 AN: 151954 Hom.: 1817 Cov.: 31

Gnomad AFR AF: 0.165

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.120

Gnomad ASJ AF: 0.232

Gnomad EAS AF: 0.00697

Gnomad SAS AF: 0.0757

Gnomad FIN AF: 0.0838

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.178

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

GnomAD4 genome AF: 0.149 AC: 22702 AN: 152074 Hom.: 1817 Cov.: 31 AF XY: 0.145 AC XY: 10765 AN XY: 74336

Gnomad4 AFR AF: 0.165

Gnomad4 AMR AF: 0.120

Gnomad4 ASJ AF: 0.232

Gnomad4 EAS AF: 0.00679

Gnomad4 SAS AF: 0.0760

Gnomad4 FIN AF: 0.0838

Gnomad4 NFE AF: 0.168

Gnomad4 OTH AF: 0.176

Alfa AF: 0.156 Hom.: 593

Bravo AF: 0.155

Asia WGS AF: 0.0590 AC: 203 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.30
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11228580; hg19: chr11-69002342;