5-40467170-T-C

Variant summary

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

The ENST00000649444.1(ENSG00000285552):n.119+3490T>C 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 0.613 in 151,792 control chromosomes in the GnomAD database, including 29,153 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 (29153 hom., cov: 32)
• Consequence: ENST00000649444.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.798

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.66 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
	ENST00000649444.1	n.119+3490T>C		intron_variant, non_coding_transcript_variant
	ENST00000649894.1	n.119+3490T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.613 AC: 93021 AN: 151674 Hom.: 29118 Cov.: 32

Gnomad AFR AF: 0.603

Gnomad AMI AF: 0.779

Gnomad AMR AF: 0.586

Gnomad ASJ AF: 0.638

Gnomad EAS AF: 0.244

Gnomad SAS AF: 0.480

Gnomad FIN AF: 0.574

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.666

Gnomad OTH AF: 0.622

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

GnomAD4 genome AF: 0.613 AC: 93114 AN: 151792 Hom.: 29153 Cov.: 32 AF XY: 0.605 AC XY: 44915 AN XY: 74182

Gnomad4 AFR AF: 0.603

Gnomad4 AMR AF: 0.586

Gnomad4 ASJ AF: 0.638

Gnomad4 EAS AF: 0.244

Gnomad4 SAS AF: 0.480

Gnomad4 FIN AF: 0.574

Gnomad4 NFE AF: 0.666

Gnomad4 OTH AF: 0.626

Alfa AF: 0.657 Hom.: 36441

Bravo AF: 0.616

Asia WGS AF: 0.409 AC: 1421 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.15
Dann	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4532399; hg19: chr5-40467272;