rs11131168

Positions:

• chr3-956829-G-A
• chr3-956829-G-C

Variant summary

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

The XR_007095784.1(LOC107986059):​n.189-759G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.389 in 151,856 control chromosomes in the GnomAD database, including 12,055 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 0.39 (12055 hom., cov: 32)
• Consequence: LOC107986059 XR_007095784.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.136

Genes affected

LOC107986059 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.631 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107986059	XR_007095784.1	n.189-759G>A		intron_variant, non_coding_transcript_variant
LOC107986059	XR_001740585.2	n.189-759G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.389 AC: 59064 AN: 151736 Hom.: 12047 Cov.: 32

Gnomad AFR AF: 0.330

Gnomad AMI AF: 0.212

Gnomad AMR AF: 0.479

Gnomad ASJ AF: 0.354

Gnomad EAS AF: 0.650

Gnomad SAS AF: 0.609

Gnomad FIN AF: 0.311

Gnomad MID AF: 0.347

Gnomad NFE AF: 0.386

Gnomad OTH AF: 0.397

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

GnomAD4 genome AF: 0.389 AC: 59099 AN: 151856 Hom.: 12055 Cov.: 32 AF XY: 0.392 AC XY: 29076 AN XY: 74204

Gnomad4 AFR AF: 0.330

Gnomad4 AMR AF: 0.479

Gnomad4 ASJ AF: 0.354

Gnomad4 EAS AF: 0.650

Gnomad4 SAS AF: 0.608

Gnomad4 FIN AF: 0.311

Gnomad4 NFE AF: 0.386

Gnomad4 OTH AF: 0.403

Alfa AF: 0.391 Hom.: 26047

Bravo AF: 0.398

Asia WGS AF: 0.630 AC: 2188 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11131168; hg19: chr3-998513;