8-92571795-A-T

Variant summary

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

The NR_125827.1(LOC102724710):n.396-2729T>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 0.204 in 151,846 control chromosomes in the GnomAD database, including 4,748 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 0.20 (4748 hom., cov: 32)
• Consequence: LOC102724710 NR_125827.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00900

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.417 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC102724710	NR_125827.1	n.396-2729T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000648652.1	n.471-2729T>A		intron_variant, non_coding_transcript_variant
	ENST00000523284.2	n.478-2729T>A		intron_variant, non_coding_transcript_variant		3
	ENST00000653143.1	n.482-2729T>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.204 AC: 30950 AN: 151728 Hom.: 4733 Cov.: 32

Gnomad AFR AF: 0.422

Gnomad AMI AF: 0.0560

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.109

Gnomad EAS AF: 0.271

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.104

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.0948

Gnomad OTH AF: 0.181

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

GnomAD4 genome AF: 0.204 AC: 31014 AN: 151846 Hom.: 4748 Cov.: 32 AF XY: 0.204 AC XY: 15113 AN XY: 74226

Gnomad4 AFR AF: 0.422

Gnomad4 AMR AF: 0.207

Gnomad4 ASJ AF: 0.109

Gnomad4 EAS AF: 0.271

Gnomad4 SAS AF: 0.126

Gnomad4 FIN AF: 0.104

Gnomad4 NFE AF: 0.0948

Gnomad4 OTH AF: 0.182

Alfa AF: 0.0526 Hom.: 50

Bravo AF: 0.220

Asia WGS AF: 0.193 AC: 671 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	3.7
Dann	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2618134; hg19: chr8-93584023;