rs586701

Positions:

• chr11-102853999-T-G

Variant summary

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

The XR_007062868.1(LOC124902741):​n.1527T>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 0.202 in 152,098 control chromosomes in the GnomAD database, including 3,218 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 0.20 (3218 hom., cov: 32)
• Consequence: LOC124902741 XR_007062868.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.784

Genes affected

LOC124902741 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.247 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124902741	XR_007062868.1	n.1527T>G		non_coding_transcript_exon_variant	1/3

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.202 AC: 30671 AN: 151980 Hom.: 3214 Cov.: 32

Gnomad AFR AF: 0.251

Gnomad AMI AF: 0.223

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.239

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.173

Gnomad FIN AF: 0.247

Gnomad MID AF: 0.290

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.198

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

GnomAD4 genome AF: 0.202 AC: 30679 AN: 152098 Hom.: 3218 Cov.: 32 AF XY: 0.201 AC XY: 14959 AN XY: 74358

Gnomad4 AFR AF: 0.251

Gnomad4 AMR AF: 0.144

Gnomad4 ASJ AF: 0.239

Gnomad4 EAS AF: 0.135

Gnomad4 SAS AF: 0.173

Gnomad4 FIN AF: 0.247

Gnomad4 NFE AF: 0.182

Gnomad4 OTH AF: 0.201

Alfa AF: 0.202 Hom.: 398

Bravo AF: 0.196

Asia WGS AF: 0.167 AC: 581 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.2
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs586701; hg19: chr11-102724730;