8-2920519-T-C

Variant names:

• chr8-2920519-T-C
• rs6989916
• ENST00000725259.1:n.1167-5246T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_168441.1(LOC105377785):​n.1167-80486T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0795 in 152,270 control chromosomes in the GnomAD database, including 531 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 0.079 (531 hom., cov: 32)
• Consequence: LOC105377785 NR_168441.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.43
• Publications: 8 publications found

Genes affected

ENSG00000253853 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.111 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_168441.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC105377785	NR_168441.1		n.1167-80486T>C		intron	N/A
	LOC105377785	NR_168442.1		n.1697+1201T>C		intron	N/A
	LOC105377785	NR_168443.1		n.1171+82755T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000253853	ENST00000725259.1		n.1167-5246T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0795 AC: 12094 AN: 152152 Hom.: 531 Cov.: 32

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.0694

Gnomad ASJ AF: 0.133

Gnomad EAS AF: 0.000773

Gnomad SAS AF: 0.0869

Gnomad FIN AF: 0.0399

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.0686

Gnomad OTH AF: 0.0908

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

GnomAD4 genome AF: 0.0795 AC: 12104 AN: 152270 Hom.: 531 Cov.: 32 AF XY: 0.0779 AC XY: 5802 AN XY: 74448

African (AFR) AF: 0.113 AC: 4716 AN: 41552

American (AMR) AF: 0.0693 AC: 1060 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.133 AC: 461 AN: 3470

East Asian (EAS) AF: 0.000775 AC: 4 AN: 5164

South Asian (SAS) AF: 0.0872 AC: 420 AN: 4818

European-Finnish (FIN) AF: 0.0399 AC: 424 AN: 10624

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.0686 AC: 4663 AN: 68020

Other (OTH) AF: 0.0937 AC: 198 AN: 2114

Alfa AF: 0.0679 Hom.: 582

Bravo AF: 0.0834

Asia WGS AF: 0.0530 AC: 185 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.77
DANN	Benign	0.59
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs6989916; hg19: chr8-2778041;