5-104863359-T-C

Position:

• chr5-104863359-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000503650.1(ENSG00000251574):​n.328+23499A>G variant causes a intron, non coding transcript 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: ENST00000503650.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.306

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000503650.1	n.328+23499A>G		intron_variant, non_coding_transcript_variant		3
	ENST00000524336.5	n.190+23499A>G		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.344

Gnomad4 AMR AF: 0.589

Gnomad4 ASJ AF: 0.454

Gnomad4 EAS AF: 0.699

Gnomad4 SAS AF: 0.663

Gnomad4 FIN AF: 0.536

Gnomad4 NFE AF: 0.520

Gnomad4 OTH AF: 0.477

Alfa AF: 0.507 Hom.: 37765

Bravo AF: 0.483

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1632744; hg19: chr5-104199060;