5-40492553-C-T

Variant names:

• chr5-40492553-C-T
• rs7714574
• ENST00000649444.1:n.242+6055C>T

Variant summary

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

The ENST00000649444.1(ENSG00000285552):​n.242+6055C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.51 in 149,760 control chromosomes in the GnomAD database, including 20,165 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 0.51 (20165 hom., cov: 25)
• Consequence: ENSG00000285552 ENST00000649444.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.662
• Publications: 11 publications found

Genes affected

ENSG00000285552 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.573 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000649444.1. 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
	ENSG00000285552	ENST00000649444.1		n.242+6055C>T		intron	N/A
	ENSG00000285552	ENST00000649894.1		n.120-11318C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.510 AC: 76315 AN: 149644 Hom.: 20146 Cov.: 25

Gnomad AFR AF: 0.466

Gnomad AMI AF: 0.717

Gnomad AMR AF: 0.490

Gnomad ASJ AF: 0.531

Gnomad EAS AF: 0.188

Gnomad SAS AF: 0.300

Gnomad FIN AF: 0.494

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.578

Gnomad OTH AF: 0.497

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

GnomAD4 genome AF: 0.510 AC: 76364 AN: 149760 Hom.: 20165 Cov.: 25 AF XY: 0.501 AC XY: 36532 AN XY: 72988

African (AFR) AF: 0.466 AC: 18910 AN: 40620

American (AMR) AF: 0.491 AC: 7373 AN: 15026

Ashkenazi Jewish (ASJ) AF: 0.531 AC: 1834 AN: 3456

East Asian (EAS) AF: 0.188 AC: 943 AN: 5022

South Asian (SAS) AF: 0.300 AC: 1417 AN: 4716

European-Finnish (FIN) AF: 0.494 AC: 4976 AN: 10076

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.578 AC: 39061 AN: 67574

Other (OTH) AF: 0.500 AC: 1037 AN: 2072

Alfa AF: 0.400 Hom.: 1079

Bravo AF: 0.510

Asia WGS AF: 0.248 AC: 865 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.4
DANN	Benign	0.29
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs7714574; hg19: chr5-40492655;