8-92572164-T-C

Position:

• chr8-92572164-T-C

Variant summary

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

The NR_125827.1(LOC102724710):​n.396-3098A>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 0.279 in 151,586 control chromosomes in the GnomAD database, including 8,833 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 0.28 (8833 hom., cov: 31)
• Consequence: LOC102724710 NR_125827.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0730

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 = 0.579 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC102724710	NR_125827.1	n.396-3098A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000648652.1	n.471-3098A>G		intron_variant, non_coding_transcript_variant
	ENST00000523284.2	n.478-3098A>G		intron_variant, non_coding_transcript_variant		3
	ENST00000653143.1	n.482-3098A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.279 AC: 42198 AN: 151472 Hom.: 8808 Cov.: 31

Gnomad AFR AF: 0.585

Gnomad AMI AF: 0.110

Gnomad AMR AF: 0.173

Gnomad ASJ AF: 0.164

Gnomad EAS AF: 0.316

Gnomad SAS AF: 0.226

Gnomad FIN AF: 0.204

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.231

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

GnomAD4 genome AF: 0.279 AC: 42274 AN: 151586 Hom.: 8833 Cov.: 31 AF XY: 0.279 AC XY: 20651 AN XY: 74072

Gnomad4 AFR AF: 0.585

Gnomad4 AMR AF: 0.173

Gnomad4 ASJ AF: 0.164

Gnomad4 EAS AF: 0.315

Gnomad4 SAS AF: 0.225

Gnomad4 FIN AF: 0.204

Gnomad4 NFE AF: 0.139

Gnomad4 OTH AF: 0.232

Alfa AF: 0.155 Hom.: 4670

Bravo AF: 0.289

Asia WGS AF: 0.274 AC: 955 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	3.4
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6993453; hg19: chr8-93584392;