8-88361098-T-G

Variant names:

• chr8-88361098-T-G
• rs36116061
• ENST00000521433.1:n.179+32046T>G

Variant summary

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

The ENST00000521433.1(ENSG00000253553):​n.179+32046T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.203 in 151,706 control chromosomes in the GnomAD database, including 3,259 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 0.20 (3259 hom., cov: 31)
• Consequence: ENSG00000253553 ENST00000521433.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00
• Publications: 2 publications found

Genes affected

ENSG00000253553 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.218 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375630	XR_001745653.3	n.224+32001T>G		intron_variant	Intron 2 of 7
LOC105375630	XR_007060996.1	n.179+32046T>G		intron_variant	Intron 2 of 2
LOC105375630	XR_007060997.1	n.123+32102T>G		intron_variant	Intron 2 of 2
LOC105375630	XR_007060998.1	n.179+32046T>G		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000253553	ENST00000521433.1	n.179+32046T>G		intron_variant	Intron 2 of 4	4
ENSG00000253553	ENST00000658256.1	n.284+32001T>G		intron_variant	Intron 2 of 3
ENSG00000253553	ENST00000658283.1	n.425+32102T>G		intron_variant	Intron 2 of 6

Frequencies

GnomAD3 genomes AF: 0.203 AC: 30824 AN: 151590 Hom.: 3245 Cov.: 31

Gnomad AFR AF: 0.210

Gnomad AMI AF: 0.357

Gnomad AMR AF: 0.219

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.0507

Gnomad SAS AF: 0.230

Gnomad FIN AF: 0.195

Gnomad MID AF: 0.163

Gnomad NFE AF: 0.206

Gnomad OTH AF: 0.219

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

GnomAD4 genome AF: 0.203 AC: 30871 AN: 151706 Hom.: 3259 Cov.: 31 AF XY: 0.202 AC XY: 14967 AN XY: 74182

African (AFR) AF: 0.211 AC: 8713 AN: 41374

American (AMR) AF: 0.219 AC: 3336 AN: 15210

Ashkenazi Jewish (ASJ) AF: 0.161 AC: 559 AN: 3468

East Asian (EAS) AF: 0.0506 AC: 262 AN: 5176

South Asian (SAS) AF: 0.229 AC: 1097 AN: 4792

European-Finnish (FIN) AF: 0.195 AC: 2048 AN: 10478

Middle Eastern (MID) AF: 0.172 AC: 50 AN: 290

European-Non Finnish (NFE) AF: 0.206 AC: 14008 AN: 67906

Other (OTH) AF: 0.225 AC: 474 AN: 2104

Alfa AF: 0.183 Hom.: 1381

Bravo AF: 0.204

Asia WGS AF: 0.195 AC: 675 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.61
DANN	Benign	0.33
PhyloP100		0.0

Splicing

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

Other links and lift over

dbSNP: rs36116061; hg19: chr8-89373327;