rs282253

chr2-224041763-G-Cchr2-224041763-G-T

Variant summary

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

The XR_007088103.1(LOC124907991):n.187G>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 0.96 in 152,324 control chromosomes in the GnomAD database, including 70,404 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 0.96 (70404 hom., cov: 33)
• Consequence: LOC124907991 XR_007088103.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.624

Genes affected

LOC124907991 (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 (NFE) allele frequency at 95% confidence interval = 0.988 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124907991	XR_007088103.1	n.187G>C		non_coding_transcript_exon_variant	2/2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.960 AC: 146138 AN: 152206 Hom.: 70358 Cov.: 33

Gnomad AFR AF: 0.911

Gnomad AMI AF: 0.978

Gnomad AMR AF: 0.977

Gnomad ASJ AF: 0.988

Gnomad EAS AF: 0.784

Gnomad SAS AF: 0.929

Gnomad FIN AF: 0.997

Gnomad MID AF: 0.984

Gnomad NFE AF: 0.994

Gnomad OTH AF: 0.968

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

GnomAD4 genome AF: 0.960 AC: 146240 AN: 152324 Hom.: 70404 Cov.: 33 AF XY: 0.960 AC XY: 71489 AN XY: 74486

Gnomad4 AFR AF: 0.911

Gnomad4 AMR AF: 0.977

Gnomad4 ASJ AF: 0.988

Gnomad4 EAS AF: 0.785

Gnomad4 SAS AF: 0.930

Gnomad4 FIN AF: 0.997

Gnomad4 NFE AF: 0.994

Gnomad4 OTH AF: 0.960

Alfa AF: 0.980 Hom.: 8519

Bravo AF: 0.956

Asia WGS AF: 0.814 AC: 2833 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	12
Dann	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs282253; hg19: chr2-224906480;