rs60587131

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124904456	XR_007066738.1	n.1792C>G		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;