8-88579854-G-T

Variant names:

• chr8-88579854-G-T
• rs11995572
• ENST00000518631.1:n.214+37024G>T

Variant summary

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

The ENST00000518631.1(ENSG00000253553):​n.214+37024G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.244 in 151,926 control chromosomes in the GnomAD database, including 5,338 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 0.24 (5338 hom., cov: 31)
• Consequence: ENSG00000253553 ENST00000518631.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.94
• Publications: 9 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=-1.11).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.392 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375629	XR_001745651.3	n.84+8537C>A		intron_variant	Intron 1 of 6
LOC105375630	XR_001745653.3	n.355+37044G>T		intron_variant	Intron 3 of 7
LOC105375630	XR_007060998.1	n.330+37024G>T		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000253553	ENST00000518631.1	n.214+37024G>T		intron_variant	Intron 1 of 1	4
ENSG00000253553	ENST00000520312.1	n.156+37095G>T		intron_variant	Intron 1 of 1	4
ENSG00000253553	ENST00000521433.1	n.310+37044G>T		intron_variant	Intron 3 of 4	4

Frequencies

GnomAD3 genomes AF: 0.243 AC: 36955 AN: 151808 Hom.: 5325 Cov.: 31

Gnomad AFR AF: 0.397

Gnomad AMI AF: 0.302

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.195

Gnomad EAS AF: 0.114

Gnomad SAS AF: 0.254

Gnomad FIN AF: 0.144

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.191

Gnomad OTH AF: 0.244

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

GnomAD4 genome AF: 0.244 AC: 36997 AN: 151926 Hom.: 5338 Cov.: 31 AF XY: 0.241 AC XY: 17905 AN XY: 74228

African (AFR) AF: 0.397 AC: 16442 AN: 41422

American (AMR) AF: 0.180 AC: 2739 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.195 AC: 678 AN: 3470

East Asian (EAS) AF: 0.115 AC: 592 AN: 5170

South Asian (SAS) AF: 0.253 AC: 1213 AN: 4792

European-Finnish (FIN) AF: 0.144 AC: 1521 AN: 10568

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.191 AC: 12952 AN: 67946

Other (OTH) AF: 0.244 AC: 515 AN: 2112

Alfa AF: 0.557 Hom.: 7413

Bravo AF: 0.249

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.30
DANN	Benign	0.094
PhyloP100		-3.9

Splicing

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

Other links and lift over

dbSNP: rs11995572; hg19: chr8-89592083;