rs11986045

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

Genes affected

ENSG00000253322 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000520426.1. 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
	ENSG00000253322	ENST00000520426.1	TSL:4	n.274-7271A>G		intron	N/A

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

African (AFR) AF: 0.510 AC: 21167 AN: 41476

American (AMR) AF: 0.0918 AC: 1404 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0518 AC: 180 AN: 3472

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5184

South Asian (SAS) AF: 0.0116 AC: 56 AN: 4826

European-Finnish (FIN) AF: 0.0314 AC: 333 AN: 10618

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0475 AC: 3229 AN: 68024

Other (OTH) AF: 0.140 AC: 296 AN: 2112

Alfa AF: 0.132 Hom.: 598

Bravo AF: 0.194

Asia WGS AF: 0.0400 AC: 140 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.5
DANN	Benign	0.62
PhyloP100		-0.29
Mutation Taster		=100/0	polymorphism

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs11986045;

hg19: chr8-58514292;