rs540006

chr2-70556290-T-C

Variant summary

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

The XR_007086906.1(LOC124907824):n.685+2898T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.058 in 149,082 control chromosomes in the GnomAD database, including 331 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 0.058 (331 hom., cov: 30)
• Consequence: LOC124907824 XR_007086906.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0710

Genes affected

LOC124907824 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.139 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124907824	XR_007086906.1	n.685+2898T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0581 AC: 8657 AN: 148984 Hom.: 329 Cov.: 30

Gnomad AFR AF: 0.0173

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0838

Gnomad ASJ AF: 0.0777

Gnomad EAS AF: 0.147

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.0712

Gnomad MID AF: 0.0609

Gnomad NFE AF: 0.0632

Gnomad OTH AF: 0.0755

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

GnomAD4 genome AF: 0.0580 AC: 8653 AN: 149082 Hom.: 331 Cov.: 30 AF XY: 0.0592 AC XY: 4294 AN XY: 72568

Gnomad4 AFR AF: 0.0172

Gnomad4 AMR AF: 0.0839

Gnomad4 ASJ AF: 0.0777

Gnomad4 EAS AF: 0.148

Gnomad4 SAS AF: 0.120

Gnomad4 FIN AF: 0.0712

Gnomad4 NFE AF: 0.0632

Gnomad4 OTH AF: 0.0753

Alfa AF: 0.0681 Hom.: 297

Bravo AF: 0.0582

Asia WGS AF: 0.141 AC: 486 AN: 3456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	12
Dann	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs540006; hg19: chr2-70783422;