rs2049048

chr11-27729039-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.3507G>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 0.168 in 152,228 control chromosomes in the GnomAD database, including 2,245 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 0.17 (2245 hom., cov: 33)
• Consequence: LOC124902652 XR_007062633.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.34

Genes affected

LOC124902652 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.3).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.22 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124902652	XR_007062633.1	n.3507G>A		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000530663.1	n.148-32517C>T		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.167 AC: 25472 AN: 152110 Hom.: 2240 Cov.: 33

Gnomad AFR AF: 0.223

Gnomad AMI AF: 0.0691

Gnomad AMR AF: 0.158

Gnomad ASJ AF: 0.0878

Gnomad EAS AF: 0.0506

Gnomad SAS AF: 0.143

Gnomad FIN AF: 0.185

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.147

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

GnomAD4 genome AF: 0.168 AC: 25501 AN: 152228 Hom.: 2245 Cov.: 33 AF XY: 0.167 AC XY: 12451 AN XY: 74424

Gnomad4 AFR AF: 0.223

Gnomad4 AMR AF: 0.158

Gnomad4 ASJ AF: 0.0878

Gnomad4 EAS AF: 0.0505

Gnomad4 SAS AF: 0.143

Gnomad4 FIN AF: 0.185

Gnomad4 NFE AF: 0.150

Gnomad4 OTH AF: 0.146

Alfa AF: 0.143 Hom.: 1709

Bravo AF: 0.165

Asia WGS AF: 0.124 AC: 431 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.30
Cadd	Benign	17
Dann	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2049048; hg19: chr11-27750586;