5-64035282-G-A

Variant names:

• chr5-64035282-G-A
• rs356562
• ENST00000845415.1:n.595-8900C>T

Variant summary

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

The ENST00000845415.1(ENSG00000309906):​n.595-8900C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.421 in 151,948 control chromosomes in the GnomAD database, including 14,055 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 0.42 (14055 hom., cov: 32)
• Consequence: ENSG00000309906 ENST00000845415.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0910
• Publications: 4 publications found

Genes affected

ENSG00000309906 (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 (AFR) allele frequency at 95% confidence interval = 0.522 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000845415.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000309906	ENST00000845415.1		n.595-8900C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.421 AC: 63977 AN: 151830 Hom.: 14037 Cov.: 32

Gnomad AFR AF: 0.528

Gnomad AMI AF: 0.589

Gnomad AMR AF: 0.389

Gnomad ASJ AF: 0.424

Gnomad EAS AF: 0.150

Gnomad SAS AF: 0.357

Gnomad FIN AF: 0.295

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.406

Gnomad OTH AF: 0.428

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

GnomAD4 genome AF: 0.421 AC: 64030 AN: 151948 Hom.: 14055 Cov.: 32 AF XY: 0.413 AC XY: 30660 AN XY: 74258

African (AFR) AF: 0.528 AC: 21872 AN: 41450

American (AMR) AF: 0.389 AC: 5924 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.424 AC: 1471 AN: 3472

East Asian (EAS) AF: 0.150 AC: 775 AN: 5170

South Asian (SAS) AF: 0.356 AC: 1711 AN: 4812

European-Finnish (FIN) AF: 0.295 AC: 3117 AN: 10564

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.406 AC: 27580 AN: 67924

Other (OTH) AF: 0.423 AC: 894 AN: 2112

Alfa AF: 0.411 Hom.: 17044

Bravo AF: 0.434

Asia WGS AF: 0.234 AC: 815 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	1.2
DANN	Benign	0.59
PhyloP100		-0.091

Splicing

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

Other links and lift over

dbSNP: rs356562; hg19: chr5-63331109;