chr5-108396257-G-A

Variant names:

• chr5-108396257-G-A
• rs1001579
• ENST00000662770.2:n.280+13849G>A

Variant summary

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

The ENST00000662770.2(ENSG00000286503):​n.280+13849G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.892 in 152,178 control chromosomes in the GnomAD database, including 60,650 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 0.89 (60650 hom., cov: 32)
• Consequence: ENSG00000286503 ENST00000662770.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.838
• Publications: 5 publications found

Genes affected

ENSG00000286503 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.948 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000662770.2. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000286503	ENST00000662770.2		n.280+13849G>A		intron	N/A
	ENSG00000286503	ENST00000835410.1		n.220+13849G>A		intron	N/A
	ENSG00000286503	ENST00000835411.1		n.253+13849G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.892 AC: 135605 AN: 152060 Hom.: 60596 Cov.: 32

Gnomad AFR AF: 0.956

Gnomad AMI AF: 0.890

Gnomad AMR AF: 0.917

Gnomad ASJ AF: 0.860

Gnomad EAS AF: 0.858

Gnomad SAS AF: 0.824

Gnomad FIN AF: 0.890

Gnomad MID AF: 0.892

Gnomad NFE AF: 0.856

Gnomad OTH AF: 0.893

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

GnomAD4 genome AF: 0.892 AC: 135719 AN: 152178 Hom.: 60650 Cov.: 32 AF XY: 0.892 AC XY: 66355 AN XY: 74372

African (AFR) AF: 0.956 AC: 39711 AN: 41554

American (AMR) AF: 0.918 AC: 14036 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.860 AC: 2984 AN: 3468

East Asian (EAS) AF: 0.857 AC: 4436 AN: 5174

South Asian (SAS) AF: 0.824 AC: 3971 AN: 4820

European-Finnish (FIN) AF: 0.890 AC: 9395 AN: 10558

Middle Eastern (MID) AF: 0.898 AC: 264 AN: 294

European-Non Finnish (NFE) AF: 0.856 AC: 58218 AN: 67990

Other (OTH) AF: 0.896 AC: 1892 AN: 2112

Alfa AF: 0.870 Hom.: 81098

Bravo AF: 0.897

Asia WGS AF: 0.838 AC: 2906 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.35
DANN	Benign	0.34
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs1001579; hg19: chr5-107731958;