rs1569175

chr2-200157231-T-Cchr2-200157231-T-G

Variant summary

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

The XR_007088012.1(LOC124906112):n.228+17339A>G 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 0.883 in 152,190 control chromosomes in the GnomAD database, including 59,802 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 0.88 (59802 hom., cov: 31)
• Consequence: LOC124906112 XR_007088012.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.609

Genes affected

LOC124906112 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.941 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124906112	XR_007088012.1	n.228+17339A>G		intron_variant, non_coding_transcript_variant
LOC124906112	XR_007088015.1	n.228+17339A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.883 AC: 134283 AN: 152072 Hom.: 59762 Cov.: 31

Gnomad AFR AF: 0.809

Gnomad AMI AF: 0.965

Gnomad AMR AF: 0.757

Gnomad ASJ AF: 0.926

Gnomad EAS AF: 0.846

Gnomad SAS AF: 0.942

Gnomad FIN AF: 0.906

Gnomad MID AF: 0.946

Gnomad NFE AF: 0.947

Gnomad OTH AF: 0.896

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

GnomAD4 genome AF: 0.883 AC: 134373 AN: 152190 Hom.: 59802 Cov.: 31 AF XY: 0.879 AC XY: 65420 AN XY: 74420

Gnomad4 AFR AF: 0.809

Gnomad4 AMR AF: 0.756

Gnomad4 ASJ AF: 0.926

Gnomad4 EAS AF: 0.846

Gnomad4 SAS AF: 0.942

Gnomad4 FIN AF: 0.906

Gnomad4 NFE AF: 0.947

Gnomad4 OTH AF: 0.898

Alfa AF: 0.934 Hom.: 143564

Bravo AF: 0.864

Asia WGS AF: 0.886 AC: 3076 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	0.80
Dann	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1569175; hg19: chr2-201021954;