rs6864913

Variant names:

• chr5-165480966-G-A
• rs6864913
• ENST00000522189.1:n.21+131916G>A

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

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

The ENST00000522189.1(ENSG00000253693):​n.21+131916G>A variant causes a intron 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: ENSG00000253693 ENST00000522189.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.20
• Publications: 3 publications found

Genes affected

ENSG00000253693 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000253693	ENST00000522189.1	n.21+131916G>A		intron_variant	Intron 1 of 1	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

African (AFR) AF: 0.130 AC: 5378 AN: 41472

American (AMR) AF: 0.311 AC: 4742 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.284 AC: 985 AN: 3468

East Asian (EAS) AF: 0.449 AC: 2313 AN: 5150

South Asian (SAS) AF: 0.418 AC: 2015 AN: 4816

European-Finnish (FIN) AF: 0.376 AC: 3976 AN: 10564

Middle Eastern (MID) AF: 0.219 AC: 64 AN: 292

European-Non Finnish (NFE) AF: 0.273 AC: 18534 AN: 67966

Other (OTH) AF: 0.267 AC: 564 AN: 2114

Alfa AF: 0.267 Hom.: 17653

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
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs6864913; hg19: chr5-164907971;