chr1-68305601-G-A

Variant names:

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

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000723549.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000294429	ENST00000723549.1		n.399+4927G>A		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6588313;

hg19: chr1-68771284;