rs6588313

Variant names:

• chr1-68305601-G-A
• rs6588313
• ENST00000723549.1:n.399+4927G>A

Your query was ambiguous. Multiple possible variants found:

• chr1-68305601-G-A
• chr1-68305601-G-C

Variant summary

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

The ENST00000723549.1(ENSG00000294429):​n.399+4927G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.622 in 152,004 control chromosomes in the GnomAD database, including 29,800 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 0.62 (29800 hom., cov: 33)
• Consequence: ENSG00000294429 ENST00000723549.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.51
• Publications: 4 publications found

Genes affected

ENSG00000294429 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.68 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378782	XR_947476.3	n.*33G>A		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000294429	ENST00000723549.1	n.399+4927G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.622 AC: 94510 AN: 151886 Hom.: 29765 Cov.: 33

Gnomad AFR AF: 0.686

Gnomad AMI AF: 0.596

Gnomad AMR AF: 0.483

Gnomad ASJ AF: 0.739

Gnomad EAS AF: 0.573

Gnomad SAS AF: 0.547

Gnomad FIN AF: 0.561

Gnomad MID AF: 0.677

Gnomad NFE AF: 0.628

Gnomad OTH AF: 0.617

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

GnomAD4 genome AF: 0.622 AC: 94592 AN: 152004 Hom.: 29800 Cov.: 33 AF XY: 0.615 AC XY: 45726 AN XY: 74298

African (AFR) AF: 0.686 AC: 28447 AN: 41442

American (AMR) AF: 0.482 AC: 7360 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.739 AC: 2562 AN: 3468

East Asian (EAS) AF: 0.573 AC: 2957 AN: 5162

South Asian (SAS) AF: 0.547 AC: 2637 AN: 4820

European-Finnish (FIN) AF: 0.561 AC: 5918 AN: 10558

Middle Eastern (MID) AF: 0.680 AC: 200 AN: 294

European-Non Finnish (NFE) AF: 0.628 AC: 42660 AN: 67978

Other (OTH) AF: 0.619 AC: 1309 AN: 2114

Alfa AF: 0.544 Hom.: 2219

Bravo AF: 0.618

Asia WGS AF: 0.531 AC: 1848 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.14
DANN	Benign	0.65
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs6588313; hg19: chr1-68771284;