rs2053481

chr8-97266695-C-T

Variant summary

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

The NR_125390.1(LOC101927066):n.471+152375G>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 0.17 in 152,108 control chromosomes in the GnomAD database, including 4,030 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 0.17 (4030 hom., cov: 32)
• Consequence: LOC101927066 NR_125390.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.462

Genes affected

LOC101927066 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.411 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101927066	NR_125390.1	n.471+152375G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.170 AC: 25860 AN: 151990 Hom.: 4028 Cov.: 32

Gnomad AFR AF: 0.417

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.125

Gnomad ASJ AF: 0.0652

Gnomad EAS AF: 0.0880

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.0528

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0670

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.170 AC: 25887 AN: 152108 Hom.: 4030 Cov.: 32 AF XY: 0.166 AC XY: 12369 AN XY: 74344

Gnomad4 AFR AF: 0.417

Gnomad4 AMR AF: 0.125

Gnomad4 ASJ AF: 0.0652

Gnomad4 EAS AF: 0.0873

Gnomad4 SAS AF: 0.132

Gnomad4 FIN AF: 0.0528

Gnomad4 NFE AF: 0.0670

Gnomad4 OTH AF: 0.122

Alfa AF: 0.127 Hom.: 311

Bravo AF: 0.186

Asia WGS AF: 0.114 AC: 396 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	0.56
Dann	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2053481; hg19: chr8-98278923;