rs958994

Variant names:

• chr5-165636879-G-A
• rs958994
• ENST00000522189.1:n.22-141098G>A

Your query was ambiguous. Multiple possible variants found:

• chr5-165636879-G-A
• chr5-165636879-G-C
• chr5-165636879-G-T

Variant summary

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

The ENST00000522189.1(ENSG00000253693):​n.22-141098G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.729 in 151,914 control chromosomes in the GnomAD database, including 40,467 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 0.73 (40467 hom., cov: 32)
• Consequence: ENSG00000253693 ENST00000522189.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.356

Genes affected

ENSG00000253693 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.808 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
ENSG00000253693	ENST00000522189.1	n.22-141098G>A		intron_variant	Intron 1 of 1	5

Frequencies

GnomAD3 genomes AF: 0.729 AC: 110642 AN: 151796 Hom.: 40437 Cov.: 32

Gnomad AFR AF: 0.779

Gnomad AMI AF: 0.680

Gnomad AMR AF: 0.743

Gnomad ASJ AF: 0.739

Gnomad EAS AF: 0.829

Gnomad SAS AF: 0.717

Gnomad FIN AF: 0.628

Gnomad MID AF: 0.750

Gnomad NFE AF: 0.704

Gnomad OTH AF: 0.744

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

GnomAD4 genome AF: 0.729 AC: 110719 AN: 151914 Hom.: 40467 Cov.: 32 AF XY: 0.725 AC XY: 53840 AN XY: 74218

Gnomad4 AFR AF: 0.779

Gnomad4 AMR AF: 0.743

Gnomad4 ASJ AF: 0.739

Gnomad4 EAS AF: 0.829

Gnomad4 SAS AF: 0.716

Gnomad4 FIN AF: 0.628

Gnomad4 NFE AF: 0.704

Gnomad4 OTH AF: 0.738

Alfa AF: 0.710 Hom.: 59793

Bravo AF: 0.741

Asia WGS AF: 0.773 AC: 2685 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.4
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs958994; hg19: chr5-165063884;