rs10751635

chr11-1062990-A-Gchr11-1062990-A-T

Variant summary

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

The XR_001748091.2(LOC107987157):n.870T>C 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 0.407 in 151,726 control chromosomes in the GnomAD database, including 12,636 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 0.41 (12636 hom., cov: 32)
• Consequence: LOC107987157 XR_001748091.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.109

Genes affected

LOC107987157 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.498 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107987157	XR_001748091.2	n.870T>C		non_coding_transcript_exon_variant	5/5
LOC107987157	XR_007062544.1	n.1242-114T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.407 AC: 61679 AN: 151606 Hom.: 12614 Cov.: 32

Gnomad AFR AF: 0.363

Gnomad AMI AF: 0.450

Gnomad AMR AF: 0.337

Gnomad ASJ AF: 0.525

Gnomad EAS AF: 0.393

Gnomad SAS AF: 0.514

Gnomad FIN AF: 0.396

Gnomad MID AF: 0.439

Gnomad NFE AF: 0.437

Gnomad OTH AF: 0.416

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

GnomAD4 genome AF: 0.407 AC: 61734 AN: 151726 Hom.: 12636 Cov.: 32 AF XY: 0.404 AC XY: 29961 AN XY: 74150

Gnomad4 AFR AF: 0.363

Gnomad4 AMR AF: 0.337

Gnomad4 ASJ AF: 0.525

Gnomad4 EAS AF: 0.393

Gnomad4 SAS AF: 0.515

Gnomad4 FIN AF: 0.396

Gnomad4 NFE AF: 0.437

Gnomad4 OTH AF: 0.417

Alfa AF: 0.434 Hom.: 21040

Bravo AF: 0.394

Asia WGS AF: 0.431 AC: 1499 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	5.6
Dann	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10751635; hg19: chr11-1062990;