rs958994

chr5-165636879-G-A

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, non coding transcript 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: ENST00000522189.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.356

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000522189.1	n.22-141098G>A		intron_variant, non_coding_transcript_variant		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;