rs2451114

chr8-97261534-G-A

Variant summary

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

The NR_125390.1(LOC101927066):n.471+157536C>T 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 0.171 in 152,094 control chromosomes in the GnomAD database, including 3,932 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 (3932 hom., cov: 31)
• Consequence: LOC101927066 NR_125390.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.537

Genes affected

LOC101927066 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.402 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101927066	NR_125390.1	n.471+157536C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.171 AC: 26021 AN: 151976 Hom.: 3932 Cov.: 31

Gnomad AFR AF: 0.407

Gnomad AMI AF: 0.00769

Gnomad AMR AF: 0.132

Gnomad ASJ AF: 0.0738

Gnomad EAS AF: 0.117

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.0527

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0699

Gnomad OTH AF: 0.139

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

GnomAD4 genome AF: 0.171 AC: 26047 AN: 152094 Hom.: 3932 Cov.: 31 AF XY: 0.168 AC XY: 12519 AN XY: 74368

Gnomad4 AFR AF: 0.407

Gnomad4 AMR AF: 0.132

Gnomad4 ASJ AF: 0.0738

Gnomad4 EAS AF: 0.116

Gnomad4 SAS AF: 0.139

Gnomad4 FIN AF: 0.0527

Gnomad4 NFE AF: 0.0700

Gnomad4 OTH AF: 0.137

Alfa AF: 0.165 Hom.: 560

Bravo AF: 0.189

Asia WGS AF: 0.128 AC: 443 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	8.6
Dann	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2451114; hg19: chr8-98273762;