rs6984609

Variant names:

• chr8-48677025-A-G
• rs6984609
• ENST00000522575.1:n.357-18399A>G

Variant summary

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

The ENST00000522575.1(ENSG00000253608):​n.357-18399A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.179 in 152,088 control chromosomes in the GnomAD database, including 5,329 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 0.18 (5329 hom., cov: 32)
• Consequence: ENSG00000253608 ENST00000522575.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.376
• Publications: 1 publications found

Genes affected

ENSG00000253608 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.481 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000522575.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC101929268	NR_105002.1		n.357-18399A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000253608	ENST00000522575.1	TSL:2	n.357-18399A>G		intron	N/A
	ENSG00000253608	ENST00000654201.1		n.58-17726A>G		intron	N/A
	ENSG00000253608	ENST00000657307.2		n.172+17842A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.179 AC: 27254 AN: 151970 Hom.: 5321 Cov.: 32

Gnomad AFR AF: 0.487

Gnomad AMI AF: 0.0670

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.0828

Gnomad EAS AF: 0.0652

Gnomad SAS AF: 0.0350

Gnomad FIN AF: 0.00952

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0506

Gnomad OTH AF: 0.178

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

GnomAD4 genome AF: 0.179 AC: 27292 AN: 152088 Hom.: 5329 Cov.: 32 AF XY: 0.172 AC XY: 12806 AN XY: 74382

African (AFR) AF: 0.486 AC: 20156 AN: 41440

American (AMR) AF: 0.154 AC: 2358 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0828 AC: 287 AN: 3466

East Asian (EAS) AF: 0.0650 AC: 335 AN: 5156

South Asian (SAS) AF: 0.0336 AC: 162 AN: 4822

European-Finnish (FIN) AF: 0.00952 AC: 101 AN: 10612

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0506 AC: 3441 AN: 67990

Other (OTH) AF: 0.176 AC: 371 AN: 2112

Alfa AF: 0.0866 Hom.: 2920

Bravo AF: 0.206

Asia WGS AF: 0.0750 AC: 263 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.97
DANN	Benign	0.48
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs6984609; hg19: chr8-49589585;