rs2451113

chr8-97261220-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+157850C>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 0.155 in 152,056 control chromosomes in the GnomAD database, including 3,125 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 (3125 hom., cov: 31)
• Consequence: LOC101927066 NR_125390.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.31

Genes affected

LOC101927066 (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 (AFR) allele frequency at 95% confidence interval = 0.353 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101927066	NR_125390.1	n.471+157850C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.155 AC: 23548 AN: 151936 Hom.: 3125 Cov.: 31

Gnomad AFR AF: 0.358

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.0652

Gnomad EAS AF: 0.116

Gnomad SAS AF: 0.139

Gnomad FIN AF: 0.0526

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0670

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.155 AC: 23569 AN: 152056 Hom.: 3125 Cov.: 31 AF XY: 0.152 AC XY: 11313 AN XY: 74328

Gnomad4 AFR AF: 0.358

Gnomad4 AMR AF: 0.121

Gnomad4 ASJ AF: 0.0652

Gnomad4 EAS AF: 0.115

Gnomad4 SAS AF: 0.139

Gnomad4 FIN AF: 0.0526

Gnomad4 NFE AF: 0.0670

Gnomad4 OTH AF: 0.119

Alfa AF: 0.119 Hom.: 254

Bravo AF: 0.170

Asia WGS AF: 0.124 AC: 432 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.12
Dann	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2451113; hg19: chr8-98273448;