rs11986045

Variant names:

• chr8-57601733-T-C
• rs11986045
• ENST00000520426.1:n.274-7271A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000520426.1(ENSG00000253322):​n.274-7271A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.175 in 152,210 control chromosomes in the GnomAD database, including 5,644 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 0.18 (5644 hom., cov: 32)
• Consequence: ENSG00000253322 ENST00000520426.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.294

Genes affected

ENSG00000253322 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 = 0.505 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000253322	ENST00000520426.1	n.274-7271A>G		intron_variant	Intron 2 of 2	4

Frequencies

GnomAD3 genomes AF: 0.175 AC: 26635 AN: 152092 Hom.: 5630 Cov.: 32

Gnomad AFR AF: 0.510

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.0921

Gnomad ASJ AF: 0.0518

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0118

Gnomad FIN AF: 0.0314

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0475

Gnomad OTH AF: 0.142

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

GnomAD4 genome AF: 0.175 AC: 26690 AN: 152210 Hom.: 5644 Cov.: 32 AF XY: 0.170 AC XY: 12676 AN XY: 74430

Gnomad4 AFR AF: 0.510

Gnomad4 AMR AF: 0.0918

Gnomad4 ASJ AF: 0.0518

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0116

Gnomad4 FIN AF: 0.0314

Gnomad4 NFE AF: 0.0475

Gnomad4 OTH AF: 0.140

Alfa AF: 0.122 Hom.: 512

Bravo AF: 0.194

Asia WGS AF: 0.0400 AC: 140 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.5
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11986045; hg19: chr8-58514292;