rs1891498

chr1-147754660-G-Achr1-147754660-G-C

Variant summary

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

The XR_922079.4(LOC102723321):n.82-22901G>A 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 0.164 in 152,224 control chromosomes in the GnomAD database, including 2,327 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 0.16 (2327 hom., cov: 33)
• Consequence: LOC102723321 XR_922079.4 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07

Genes affected

LOC102723321 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.216 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC102723321	XR_922079.4	n.82-22901G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.164 AC: 24926 AN: 152106 Hom.: 2326 Cov.: 33

Gnomad AFR AF: 0.0920

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.149

Gnomad ASJ AF: 0.130

Gnomad EAS AF: 0.0792

Gnomad SAS AF: 0.0507

Gnomad FIN AF: 0.211

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.219

Gnomad OTH AF: 0.165

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

GnomAD4 genome AF: 0.164 AC: 24934 AN: 152224 Hom.: 2327 Cov.: 33 AF XY: 0.159 AC XY: 11863 AN XY: 74412

Gnomad4 AFR AF: 0.0920

Gnomad4 AMR AF: 0.148

Gnomad4 ASJ AF: 0.130

Gnomad4 EAS AF: 0.0788

Gnomad4 SAS AF: 0.0516

Gnomad4 FIN AF: 0.211

Gnomad4 NFE AF: 0.219

Gnomad4 OTH AF: 0.164

Alfa AF: 0.189 Hom.: 1478

Bravo AF: 0.158

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.13

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1891498; hg19: chr1-147226791;