rs2439702

Positions:

• chr8-97260419-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+158651G>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 0.16 in 152,024 control chromosomes in the GnomAD database, including 3,496 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 (3496 hom., cov: 30)
• Consequence: LOC101927066 NR_125390.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.549

Genes affected

LOC101927066 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.379 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC101927066	NR_125390.1	n.471+158651G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.160 AC: 24371 AN: 151906 Hom.: 3495 Cov.: 30

Gnomad AFR AF: 0.384

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.120

Gnomad ASJ AF: 0.0651

Gnomad EAS AF: 0.0878

Gnomad SAS AF: 0.130

Gnomad FIN AF: 0.0524

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0670

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.160 AC: 24397 AN: 152024 Hom.: 3496 Cov.: 30 AF XY: 0.157 AC XY: 11682 AN XY: 74336

Gnomad4 AFR AF: 0.384

Gnomad4 AMR AF: 0.120

Gnomad4 ASJ AF: 0.0651

Gnomad4 EAS AF: 0.0870

Gnomad4 SAS AF: 0.129

Gnomad4 FIN AF: 0.0524

Gnomad4 NFE AF: 0.0670

Gnomad4 OTH AF: 0.120

Alfa AF: 0.103 Hom.: 319

Bravo AF: 0.176

Asia WGS AF: 0.111 AC: 387 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.74
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2439702; hg19: chr8-98272647;