ENST00000523205.1:n.87-6793A>G

Variant names:

• chr5-173437107-A-G
• rs6878606
• ENST00000523205.1:n.87-6793A>G

Variant summary

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

The ENST00000523205.1(ENSG00000253968):​n.87-6793A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.42 in 152,078 control chromosomes in the GnomAD database, including 15,098 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 0.42 (15098 hom., cov: 32)
• Consequence: ENSG00000253968 ENST00000523205.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.75
• Publications: 2 publications found

Genes affected

ENSG00000253968 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.65 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377732	XR_001743001.1	n.162-6793A>G		intron_variant	Intron 1 of 14
LOC105377732	XR_007059057.1	n.161-6793A>G		intron_variant	Intron 1 of 17

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000253968	ENST00000523205.1	n.87-6793A>G		intron_variant	Intron 1 of 3	3
ENSG00000253968	ENST00000654783.1	n.135-6793A>G		intron_variant	Intron 2 of 4
ENSG00000253968	ENST00000655905.1	n.225-6793A>G		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.420 AC: 63799 AN: 151960 Hom.: 15058 Cov.: 32

Gnomad AFR AF: 0.656

Gnomad AMI AF: 0.296

Gnomad AMR AF: 0.341

Gnomad ASJ AF: 0.348

Gnomad EAS AF: 0.381

Gnomad SAS AF: 0.352

Gnomad FIN AF: 0.379

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.314

Gnomad OTH AF: 0.400

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

GnomAD4 genome AF: 0.420 AC: 63906 AN: 152078 Hom.: 15098 Cov.: 32 AF XY: 0.421 AC XY: 31300 AN XY: 74314

African (AFR) AF: 0.656 AC: 27199 AN: 41456

American (AMR) AF: 0.342 AC: 5222 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.348 AC: 1206 AN: 3466

East Asian (EAS) AF: 0.382 AC: 1978 AN: 5178

South Asian (SAS) AF: 0.351 AC: 1693 AN: 4818

European-Finnish (FIN) AF: 0.379 AC: 4013 AN: 10584

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.314 AC: 21361 AN: 67972

Other (OTH) AF: 0.402 AC: 850 AN: 2112

Alfa AF: 0.342 Hom.: 40647

Bravo AF: 0.427

Asia WGS AF: 0.353 AC: 1226 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.075
DANN	Benign	0.31
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs6878606; hg19: chr5-172864110;