5-34448754-A-G

Variant names:

• chr5-34448754-A-G
• rs12659880
• ENST00000806125.1:n.314-20021A>G

Variant summary

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

The ENST00000806125.1(ENSG00000304753):​n.314-20021A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.419 in 152,048 control chromosomes in the GnomAD database, including 13,721 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 (13721 hom., cov: 32)
• Consequence: ENSG00000304753 ENST00000806125.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.237
• Publications: 0 publications found

Genes affected

ENSG00000304753 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.566 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000806125.1. 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
	ENSG00000304753	ENST00000806125.1		n.314-20021A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.418 AC: 63582 AN: 151930 Hom.: 13705 Cov.: 32

Gnomad AFR AF: 0.477

Gnomad AMI AF: 0.391

Gnomad AMR AF: 0.333

Gnomad ASJ AF: 0.371

Gnomad EAS AF: 0.302

Gnomad SAS AF: 0.583

Gnomad FIN AF: 0.426

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.402

Gnomad OTH AF: 0.390

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

GnomAD4 genome AF: 0.419 AC: 63637 AN: 152048 Hom.: 13721 Cov.: 32 AF XY: 0.422 AC XY: 31379 AN XY: 74330

African (AFR) AF: 0.477 AC: 19800 AN: 41466

American (AMR) AF: 0.332 AC: 5076 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.371 AC: 1288 AN: 3472

East Asian (EAS) AF: 0.302 AC: 1557 AN: 5158

South Asian (SAS) AF: 0.584 AC: 2815 AN: 4822

European-Finnish (FIN) AF: 0.426 AC: 4499 AN: 10560

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.402 AC: 27318 AN: 67978

Other (OTH) AF: 0.392 AC: 828 AN: 2112

Alfa AF: 0.404 Hom.: 2602

Bravo AF: 0.409

Asia WGS AF: 0.475 AC: 1654 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.61
DANN	Benign	0.57
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs12659880; hg19: chr5-34448859;