rs61768480

Positions:

• chr1-1167770-G-A

Variant summary

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

The XR_007065348.1(LOC124903818):​n.4518G>A 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 0.237 in 464,264 control chromosomes in the GnomAD database, including 14,569 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 0.23 (4562 hom., cov: 33)
  • Exomes 𝑓: 0.24 (10007 hom.)
• Consequence: LOC124903818 XR_007065348.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.296

Genes affected

LOC124903818 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.279 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124903818	XR_007065348.1	n.4518G>A		non_coding_transcript_exon_variant	2/2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.230 AC: 34991 AN: 151970 Hom.: 4561 Cov.: 33

Gnomad AFR AF: 0.174

Gnomad AMI AF: 0.213

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.198

Gnomad EAS AF: 0.0309

Gnomad SAS AF: 0.188

Gnomad FIN AF: 0.341

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.282

Gnomad OTH AF: 0.223

GnomAD4 exome AF: 0.241 AC: 75091 AN: 312176 Hom.: 10007 AF XY: 0.239 AC XY: 42282 AN XY: 176630

Gnomad4 AFR exome AF: 0.176

Gnomad4 AMR exome AF: 0.118

Gnomad4 ASJ exome AF: 0.189

Gnomad4 EAS exome AF: 0.0286

Gnomad4 SAS exome AF: 0.203

Gnomad4 FIN exome AF: 0.329

Gnomad4 NFE exome AF: 0.281

Gnomad4 OTH exome AF: 0.239

GnomAD4 genome AF: 0.230 AC: 35011 AN: 152088 Hom.: 4562 Cov.: 33 AF XY: 0.230 AC XY: 17119 AN XY: 74352

Gnomad4 AFR AF: 0.174

Gnomad4 AMR AF: 0.165

Gnomad4 ASJ AF: 0.198

Gnomad4 EAS AF: 0.0308

Gnomad4 SAS AF: 0.188

Gnomad4 FIN AF: 0.341

Gnomad4 NFE AF: 0.282

Gnomad4 OTH AF: 0.219

Alfa AF: 0.262 Hom.: 686

Bravo AF: 0.211

Asia WGS AF: 0.101 AC: 350 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.95
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs61768480; hg19: chr1-1103150;