XR_007066738.1:n.1792C>G

Variant names:

• chr1-173491015-G-C
• rs60587131
• XR_007066738.1:n.1792C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007066738.1(LOC124904456):​n.1792C>G 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 0.0488 in 152,162 control chromosomes in the GnomAD database, including 391 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 0.049 (391 hom., cov: 32)
• Consequence: LOC124904456 XR_007066738.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.117
• Publications: 1 publications found

Genes affected

LOC124904456 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.272 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0488 AC: 7422 AN: 152044 Hom.: 389 Cov.: 32

Gnomad AFR AF: 0.0107

Gnomad AMI AF: 0.0658

Gnomad AMR AF: 0.0344

Gnomad ASJ AF: 0.0352

Gnomad EAS AF: 0.284

Gnomad SAS AF: 0.0973

Gnomad FIN AF: 0.0618

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0525

Gnomad OTH AF: 0.0470

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

GnomAD4 genome AF: 0.0488 AC: 7431 AN: 152162 Hom.: 391 Cov.: 32 AF XY: 0.0508 AC XY: 3776 AN XY: 74388

African (AFR) AF: 0.0107 AC: 445 AN: 41532

American (AMR) AF: 0.0343 AC: 524 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0352 AC: 122 AN: 3462

East Asian (EAS) AF: 0.284 AC: 1471 AN: 5176

South Asian (SAS) AF: 0.0978 AC: 472 AN: 4824

European-Finnish (FIN) AF: 0.0618 AC: 653 AN: 10574

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0525 AC: 3573 AN: 68010

Other (OTH) AF: 0.0503 AC: 106 AN: 2106

Alfa AF: 0.0483 Hom.: 30

Bravo AF: 0.0442

Asia WGS AF: 0.199 AC: 690 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	1.6
DANN	Benign	0.75
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs60587131; hg19: chr1-173460154;