rs11167821

Variant names:

• chr5-143595079-A-G
• rs11167821
• ENST00000661617.1:n.424-2939A>G

Your query was ambiguous. Multiple possible variants found:

• chr5-143595079-A-G
• chr5-143595079-A-T

Variant summary

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

The ENST00000661617.1(ENSG00000251205):​n.424-2939A>G 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 152,062 control chromosomes in the GnomAD database, including 5,088 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 (5088 hom., cov: 32)
• Consequence: ENSG00000251205 ENST00000661617.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.832
• Publications: 7 publications found

Genes affected

ENSG00000251205 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.53).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.319 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000661617.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000251205	ENST00000661617.1		n.424-2939A>G		intron	N/A
	ENSG00000251205	ENST00000833525.1		n.298-2939A>G		intron	N/A
	ENSG00000251205	ENST00000833526.1		n.173-2939A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.244 AC: 37035 AN: 151944 Hom.: 5078 Cov.: 32

Gnomad AFR AF: 0.324

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.0196

Gnomad SAS AF: 0.0863

Gnomad FIN AF: 0.204

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.256

Gnomad OTH AF: 0.203

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

GnomAD4 genome AF: 0.244 AC: 37089 AN: 152062 Hom.: 5088 Cov.: 32 AF XY: 0.235 AC XY: 17491 AN XY: 74348

African (AFR) AF: 0.324 AC: 13428 AN: 41448

American (AMR) AF: 0.163 AC: 2486 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.115 AC: 399 AN: 3466

East Asian (EAS) AF: 0.0199 AC: 103 AN: 5182

South Asian (SAS) AF: 0.0849 AC: 410 AN: 4828

European-Finnish (FIN) AF: 0.204 AC: 2156 AN: 10572

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.256 AC: 17413 AN: 67960

Other (OTH) AF: 0.203 AC: 429 AN: 2114

Alfa AF: 0.242 Hom.: 18861

Bravo AF: 0.247

Asia WGS AF: 0.0780 AC: 273 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.53
CADD	Benign	0.64
DANN	Benign	0.54
PhyloP100		-0.83

Splicing

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

Other links and lift over

dbSNP: rs11167821; hg19: chr5-142974644;