rs6864913

Positions:

• chr5-165480966-G-A
• chr5-165480966-G-C

Variant summary

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

The ENST00000522189.1(ENSG00000253693):​n.21+131916G>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 0.256 in 152,010 control chromosomes in the GnomAD database, including 5,696 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 0.26 (5696 hom., cov: 32)
• Consequence: ENST00000522189.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.20

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.434 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000522189.1	n.21+131916G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.256 AC: 38936 AN: 151892 Hom.: 5694 Cov.: 32

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.417

Gnomad AMR AF: 0.310

Gnomad ASJ AF: 0.284

Gnomad EAS AF: 0.449

Gnomad SAS AF: 0.419

Gnomad FIN AF: 0.376

Gnomad MID AF: 0.210

Gnomad NFE AF: 0.273

Gnomad OTH AF: 0.270

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

GnomAD4 genome AF: 0.256 AC: 38950 AN: 152010 Hom.: 5696 Cov.: 32 AF XY: 0.266 AC XY: 19784 AN XY: 74284

Gnomad4 AFR AF: 0.130

Gnomad4 AMR AF: 0.311

Gnomad4 ASJ AF: 0.284

Gnomad4 EAS AF: 0.449

Gnomad4 SAS AF: 0.418

Gnomad4 FIN AF: 0.376

Gnomad4 NFE AF: 0.273

Gnomad4 OTH AF: 0.267

Alfa AF: 0.275 Hom.: 12312

Bravo AF: 0.248

Asia WGS AF: 0.406 AC: 1413 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	15
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6864913; hg19: chr5-164907971;