rs11995572

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000518631.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000253553	ENST00000518631.1	TSL:4	n.214+37024G>T		intron	N/A
	ENSG00000253553	ENST00000520312.1	TSL:4	n.156+37095G>T		intron	N/A
	ENSG00000253553	ENST00000521433.1	TSL:4	n.310+37044G>T		intron	N/A

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 v4.9

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;