rs2439700

Positions:

• chr8-97264940-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+154130C>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 0.173 in 152,120 control chromosomes in the GnomAD database, including 4,247 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 (4247 hom., cov: 32)
• Consequence: LOC101927066 NR_125390.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.187

Genes affected

LOC101927066 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.423 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC101927066	NR_125390.1	n.471+154130C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.173 AC: 26360 AN: 152002 Hom.: 4245 Cov.: 32

Gnomad AFR AF: 0.428

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.126

Gnomad ASJ AF: 0.0652

Gnomad EAS AF: 0.0886

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.0526

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0671

Gnomad OTH AF: 0.127

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

GnomAD4 genome AF: 0.173 AC: 26386 AN: 152120 Hom.: 4247 Cov.: 32 AF XY: 0.169 AC XY: 12594 AN XY: 74362

Gnomad4 AFR AF: 0.428

Gnomad4 AMR AF: 0.126

Gnomad4 ASJ AF: 0.0652

Gnomad4 EAS AF: 0.0878

Gnomad4 SAS AF: 0.131

Gnomad4 FIN AF: 0.0526

Gnomad4 NFE AF: 0.0671

Gnomad4 OTH AF: 0.124

Alfa AF: 0.108 Hom.: 371

Bravo AF: 0.190

Asia WGS AF: 0.115 AC: 400 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.8
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2439700; hg19: chr8-98277168;