rs1491850

chr11-27728178-T-C

Variant summary

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

The XR_007062633.1(LOC124902652):n.2646T>C 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 0.374 in 152,106 control chromosomes in the GnomAD database, including 11,090 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 0.37 (11090 hom., cov: 33)
• Consequence: LOC124902652 XR_007062633.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.763

Genes affected

LOC124902652 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.451 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124902652	XR_007062633.1	n.2646T>C		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000530663.1	n.148-31656A>G		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.374 AC: 56811 AN: 151988 Hom.: 11081 Cov.: 33

Gnomad AFR AF: 0.265

Gnomad AMI AF: 0.481

Gnomad AMR AF: 0.368

Gnomad ASJ AF: 0.418

Gnomad EAS AF: 0.466

Gnomad SAS AF: 0.391

Gnomad FIN AF: 0.426

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.421

Gnomad OTH AF: 0.385

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

GnomAD4 genome AF: 0.374 AC: 56850 AN: 152106 Hom.: 11090 Cov.: 33 AF XY: 0.373 AC XY: 27723 AN XY: 74356

Gnomad4 AFR AF: 0.265

Gnomad4 AMR AF: 0.369

Gnomad4 ASJ AF: 0.418

Gnomad4 EAS AF: 0.466

Gnomad4 SAS AF: 0.390

Gnomad4 FIN AF: 0.426

Gnomad4 NFE AF: 0.421

Gnomad4 OTH AF: 0.386

Alfa AF: 0.413 Hom.: 17634

Bravo AF: 0.369

Asia WGS AF: 0.415 AC: 1440 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	9.7
Dann	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1491850; hg19: chr11-27749725;