rs1365057

chr11-35088128-G-Achr11-35088128-G-Cchr11-35088128-G-T

Variant summary

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

The XR_931194.2(LOC105376627):n.4055-310G>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 0.242 in 152,150 control chromosomes in the GnomAD database, including 4,636 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 0.24 (4636 hom., cov: 32)
• Consequence: LOC105376627 XR_931194.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.891

Genes affected

LOC105376627 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.378 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105376627	XR_931194.2	n.4055-310G>A		intron_variant, non_coding_transcript_variant
LOC105376627	XR_001748184.2	n.99G>A		non_coding_transcript_exon_variant	1/3
LOC105376627	XR_931193.3	n.99G>A		non_coding_transcript_exon_variant	1/4

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.243 AC: 36873 AN: 152032 Hom.: 4648 Cov.: 32

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.277

Gnomad AMR AF: 0.285

Gnomad ASJ AF: 0.310

Gnomad EAS AF: 0.393

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.254

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.230

Gnomad OTH AF: 0.248

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

GnomAD4 genome AF: 0.242 AC: 36871 AN: 152150 Hom.: 4636 Cov.: 32 AF XY: 0.242 AC XY: 17996 AN XY: 74392

Gnomad4 AFR AF: 0.229

Gnomad4 AMR AF: 0.285

Gnomad4 ASJ AF: 0.310

Gnomad4 EAS AF: 0.392

Gnomad4 SAS AF: 0.155

Gnomad4 FIN AF: 0.254

Gnomad4 NFE AF: 0.230

Gnomad4 OTH AF: 0.245

Alfa AF: 0.233 Hom.: 8403

Bravo AF: 0.246

Asia WGS AF: 0.292 AC: 1014 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	1.7
Dann	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1365057; hg19: chr11-35109675;