11-27726124-G-A

Position:

• chr11-27726124-G-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The XR_007062633.1(LOC124902652):​n.592G>A 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 0.156 in 152,076 control chromosomes in the GnomAD database, including 2,130 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 0.16 (2130 hom., cov: 32)
• Consequence: LOC124902652 XR_007062633.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.437

Genes affected

LOC124902652 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.26).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.193 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124902652	XR_007062633.1	n.592G>A		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000530663.1	n.148-29602C>T		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.156 AC: 23757 AN: 151958 Hom.: 2131 Cov.: 32

Gnomad AFR AF: 0.0916

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.139

Gnomad EAS AF: 0.0119

Gnomad SAS AF: 0.0954

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.131

Gnomad NFE AF: 0.196

Gnomad OTH AF: 0.165

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

GnomAD4 genome AF: 0.156 AC: 23763 AN: 152076 Hom.: 2130 Cov.: 32 AF XY: 0.155 AC XY: 11494 AN XY: 74324

Gnomad4 AFR AF: 0.0915

Gnomad4 AMR AF: 0.165

Gnomad4 ASJ AF: 0.139

Gnomad4 EAS AF: 0.0120

Gnomad4 SAS AF: 0.0957

Gnomad4 FIN AF: 0.249

Gnomad4 NFE AF: 0.196

Gnomad4 OTH AF: 0.167

Alfa AF: 0.169 Hom.: 402

Bravo AF: 0.150

Asia WGS AF: 0.0940 AC: 327 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.26
CADD	Benign	18
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12288512; hg19: chr11-27747671;