5-104863359-T-C

Variant names:

• chr5-104863359-T-C
• rs1632744
• ENST00000503650.1:n.328+23499A>G

Variant summary

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

The ENST00000503650.1(ENSG00000251574):​n.328+23499A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.488 in 151,904 control chromosomes in the GnomAD database, including 18,976 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 0.49 (18976 hom., cov: 32)
• Consequence: ENSG00000251574 ENST00000503650.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.306
• Publications: 2 publications found

Genes affected

ENSG00000251574 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.68 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000503650.1. 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
	ENSG00000251574	ENST00000503650.1	TSL:3	n.328+23499A>G		intron	N/A
	ENSG00000251574	ENST00000524336.5	TSL:3	n.190+23499A>G		intron	N/A
	ENSG00000251574	ENST00000807455.1		n.133+23499A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.488 AC: 74079 AN: 151786 Hom.: 18958 Cov.: 32

Gnomad AFR AF: 0.344

Gnomad AMI AF: 0.439

Gnomad AMR AF: 0.589

Gnomad ASJ AF: 0.454

Gnomad EAS AF: 0.700

Gnomad SAS AF: 0.663

Gnomad FIN AF: 0.536

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.520

Gnomad OTH AF: 0.477

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

GnomAD4 genome AF: 0.488 AC: 74132 AN: 151904 Hom.: 18976 Cov.: 32 AF XY: 0.494 AC XY: 36687 AN XY: 74218

African (AFR) AF: 0.344 AC: 14272 AN: 41476

American (AMR) AF: 0.589 AC: 8963 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.454 AC: 1574 AN: 3468

East Asian (EAS) AF: 0.699 AC: 3595 AN: 5142

South Asian (SAS) AF: 0.663 AC: 3199 AN: 4822

European-Finnish (FIN) AF: 0.536 AC: 5653 AN: 10550

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.520 AC: 35348 AN: 67920

Other (OTH) AF: 0.477 AC: 1007 AN: 2110

Alfa AF: 0.509 Hom.: 53067

Bravo AF: 0.483

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	4.3
DANN	Benign	0.54
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs1632744; hg19: chr5-104199060;