rs11167821

Positions:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000251205 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105378209	XR_944375.1	n.176-2939A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000251205	ENST00000661617.1	n.424-2939A>G		intron_variant

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

Gnomad4 AFR AF: 0.324

Gnomad4 AMR AF: 0.163

Gnomad4 ASJ AF: 0.115

Gnomad4 EAS AF: 0.0199

Gnomad4 SAS AF: 0.0849

Gnomad4 FIN AF: 0.204

Gnomad4 NFE AF: 0.256

Gnomad4 OTH AF: 0.203

Alfa AF: 0.232 Hom.: 7790

Bravo AF: 0.247

Asia WGS AF: 0.0780 AC: 273 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11167821; hg19: chr5-142974644;