chr3-68959094-G-A

Variant names:

• chr3-68959094-G-A
• rs7427984
• ENST00000723547.1:n.59+5610G>A

Variant summary

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

The ENST00000723547.1(ENSG00000294428):​n.59+5610G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.479 in 151,930 control chromosomes in the GnomAD database, including 18,517 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 0.48 (18517 hom., cov: 31)
• Consequence: ENSG00000294428 ENST00000723547.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49
• Publications: 4 publications found

Genes affected

ENSG00000294428 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.564 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000723547.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000294428	ENST00000723547.1		n.59+5610G>A		intron	N/A
	ENSG00000294428	ENST00000723548.1		n.85+5610G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.480 AC: 72806 AN: 151812 Hom.: 18511 Cov.: 31

Gnomad AFR AF: 0.425

Gnomad AMI AF: 0.492

Gnomad AMR AF: 0.423

Gnomad ASJ AF: 0.613

Gnomad EAS AF: 0.0847

Gnomad SAS AF: 0.323

Gnomad FIN AF: 0.409

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.569

Gnomad OTH AF: 0.524

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

GnomAD4 genome AF: 0.479 AC: 72832 AN: 151930 Hom.: 18517 Cov.: 31 AF XY: 0.465 AC XY: 34523 AN XY: 74260

African (AFR) AF: 0.425 AC: 17593 AN: 41416

American (AMR) AF: 0.422 AC: 6445 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.613 AC: 2125 AN: 3468

East Asian (EAS) AF: 0.0845 AC: 437 AN: 5170

South Asian (SAS) AF: 0.321 AC: 1546 AN: 4816

European-Finnish (FIN) AF: 0.409 AC: 4312 AN: 10542

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.569 AC: 38640 AN: 67928

Other (OTH) AF: 0.528 AC: 1110 AN: 2104

Alfa AF: 0.534 Hom.: 17458

Bravo AF: 0.478

Asia WGS AF: 0.282 AC: 981 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.011
DANN	Benign	0.57
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs7427984; hg19: chr3-69008245;