rs2451110

Positions:

• chr8-97253033-T-C

Variant summary

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

The NR_125390.1(LOC101927066):​n.471+166037A>G 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 0.0276 in 152,290 control chromosomes in the GnomAD database, including 116 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 0.028 (116 hom., cov: 33)
• Consequence: LOC101927066 NR_125390.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.43

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 (EAS) allele frequency at 95% confidence interval = 0.0935 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC101927066	NR_125390.1	n.471+166037A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0274 AC: 4170 AN: 152172 Hom.: 114 Cov.: 33

Gnomad AFR AF: 0.0353

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0337

Gnomad ASJ AF: 0.0234

Gnomad EAS AF: 0.100

Gnomad SAS AF: 0.0924

Gnomad FIN AF: 0.0149

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0138

Gnomad OTH AF: 0.0215

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

GnomAD4 genome AF: 0.0276 AC: 4196 AN: 152290 Hom.: 116 Cov.: 33 AF XY: 0.0293 AC XY: 2185 AN XY: 74458

Gnomad4 AFR AF: 0.0356

Gnomad4 AMR AF: 0.0339

Gnomad4 ASJ AF: 0.0234

Gnomad4 EAS AF: 0.101

Gnomad4 SAS AF: 0.0929

Gnomad4 FIN AF: 0.0149

Gnomad4 NFE AF: 0.0138

Gnomad4 OTH AF: 0.0232

Alfa AF: 0.0217 Hom.: 13

Bravo AF: 0.0283

Asia WGS AF: 0.125 AC: 433 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	0.024
DANN	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2451110; hg19: chr8-98265261;