5-4035819-T-C

Position:

• chr5-4035819-T-C

Variant summary

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

The ENST00000506305.1(ENSG00000249994):​n.279+1416A>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 0.612 in 151,986 control chromosomes in the GnomAD database, including 29,624 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 0.61 (29624 hom., cov: 32)
• Consequence: ENST00000506305.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.263

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 = 0.781 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000506305.1	n.279+1416A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.612 AC: 92894 AN: 151866 Hom.: 29585 Cov.: 32

Gnomad AFR AF: 0.788

Gnomad AMI AF: 0.491

Gnomad AMR AF: 0.587

Gnomad ASJ AF: 0.612

Gnomad EAS AF: 0.769

Gnomad SAS AF: 0.610

Gnomad FIN AF: 0.566

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.507

Gnomad OTH AF: 0.603

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

GnomAD4 genome AF: 0.612 AC: 92984 AN: 151986 Hom.: 29624 Cov.: 32 AF XY: 0.615 AC XY: 45653 AN XY: 74282

Gnomad4 AFR AF: 0.788

Gnomad4 AMR AF: 0.586

Gnomad4 ASJ AF: 0.612

Gnomad4 EAS AF: 0.769

Gnomad4 SAS AF: 0.610

Gnomad4 FIN AF: 0.566

Gnomad4 NFE AF: 0.507

Gnomad4 OTH AF: 0.601

Alfa AF: 0.562 Hom.: 3053

Bravo AF: 0.622

Asia WGS AF: 0.679 AC: 2361 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.3
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs521660; hg19: chr5-4035932;