chr8-23080343-G-A

Position:

• chr8-23080343-G-A

Variant summary

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

The NR_038873.1(LOC286059):​n.193-642G>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 0.839 in 152,166 control chromosomes in the GnomAD database, including 53,931 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 0.84 (53931 hom., cov: 31)
• Consequence: LOC286059 NR_038873.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.899

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.913 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC286059	NR_038873.1	n.193-642G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000501897.1	n.193-642G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.839 AC: 127588 AN: 152048 Hom.: 53881 Cov.: 31

Gnomad AFR AF: 0.921

Gnomad AMI AF: 0.865

Gnomad AMR AF: 0.869

Gnomad ASJ AF: 0.735

Gnomad EAS AF: 0.823

Gnomad SAS AF: 0.891

Gnomad FIN AF: 0.770

Gnomad MID AF: 0.778

Gnomad NFE AF: 0.796

Gnomad OTH AF: 0.837

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

GnomAD4 genome AF: 0.839 AC: 127696 AN: 152166 Hom.: 53931 Cov.: 31 AF XY: 0.840 AC XY: 62491 AN XY: 74392

Gnomad4 AFR AF: 0.921

Gnomad4 AMR AF: 0.869

Gnomad4 ASJ AF: 0.735

Gnomad4 EAS AF: 0.823

Gnomad4 SAS AF: 0.891

Gnomad4 FIN AF: 0.770

Gnomad4 NFE AF: 0.796

Gnomad4 OTH AF: 0.838

Alfa AF: 0.815 Hom.: 27792

Bravo AF: 0.852

Asia WGS AF: 0.879 AC: 3060 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.12
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4268128; hg19: chr8-22937856;