rs6993453

Variant names:

• chr8-92572164-T-C
• rs6993453
• ENST00000523284.3:n.480-3098A>G

Variant summary

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

The ENST00000523284.3(ENSG00000253634):​n.480-3098A>G variant causes a intron 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: ENSG00000253634 ENST00000523284.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0730
• Publications: 1 publications found

Genes affected

ENSG00000253634 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000523284.3. 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
	LOC102724710	NR_125827.1		n.396-3098A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000253634	ENST00000523284.3	TSL:3	n.480-3098A>G		intron	N/A
	ENSG00000253634	ENST00000648652.1		n.471-3098A>G		intron	N/A
	ENSG00000253634	ENST00000653143.2		n.484-3098A>G		intron	N/A

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

African (AFR) AF: 0.585 AC: 24166 AN: 41312

American (AMR) AF: 0.173 AC: 2629 AN: 15190

Ashkenazi Jewish (ASJ) AF: 0.164 AC: 569 AN: 3466

East Asian (EAS) AF: 0.315 AC: 1622 AN: 5142

South Asian (SAS) AF: 0.225 AC: 1081 AN: 4804

European-Finnish (FIN) AF: 0.204 AC: 2148 AN: 10504

Middle Eastern (MID) AF: 0.161 AC: 47 AN: 292

European-Non Finnish (NFE) AF: 0.139 AC: 9426 AN: 67870

Other (OTH) AF: 0.232 AC: 486 AN: 2096

Alfa AF: 0.178 Hom.: 15324

Bravo AF: 0.289

Asia WGS AF: 0.274 AC: 955 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.4
DANN	Benign	0.28
PhyloP100		-0.073
Mutation Taster		=100/0	polymorphism

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6993453;

hg19: chr8-93584392;