11-35067136-T-C

Position:

• chr11-35067136-T-C

Variant summary

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

The XR_001748180.2(LOC105376626):​n.56A>G 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 0.53 in 152,046 control chromosomes in the GnomAD database, including 22,004 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 0.53 (22004 hom., cov: 32)
• Consequence: LOC105376626 XR_001748180.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.205

Genes affected

LOC105376626 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.734 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105376626	XR_001748180.2	n.56A>G		non_coding_transcript_exon_variant	1/4
LOC105376626	XR_007062653.1	n.56A>G		non_coding_transcript_exon_variant	1/5
LOC105376626	XR_007062654.1	n.56A>G		non_coding_transcript_exon_variant	1/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000687081.1	n.57A>G		non_coding_transcript_exon_variant	1/2

Frequencies

GnomAD3 genomes AF: 0.530 AC: 80553 AN: 151928 Hom.: 21998 Cov.: 32

Gnomad AFR AF: 0.400

Gnomad AMI AF: 0.568

Gnomad AMR AF: 0.610

Gnomad ASJ AF: 0.614

Gnomad EAS AF: 0.754

Gnomad SAS AF: 0.691

Gnomad FIN AF: 0.522

Gnomad MID AF: 0.624

Gnomad NFE AF: 0.558

Gnomad OTH AF: 0.560

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

GnomAD4 genome AF: 0.530 AC: 80576 AN: 152046 Hom.: 22004 Cov.: 32 AF XY: 0.535 AC XY: 39719 AN XY: 74308

Gnomad4 AFR AF: 0.399

Gnomad4 AMR AF: 0.611

Gnomad4 ASJ AF: 0.614

Gnomad4 EAS AF: 0.753

Gnomad4 SAS AF: 0.690

Gnomad4 FIN AF: 0.522

Gnomad4 NFE AF: 0.558

Gnomad4 OTH AF: 0.563

Alfa AF: 0.559 Hom.: 31477

Bravo AF: 0.528

Asia WGS AF: 0.690 AC: 2399 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.3
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2732547; hg19: chr11-35088683;