chr5-40798542-C-T

Position:

• chr5-40798542-C-T

Variant summary

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

The ENST00000691528.2(ENSG00000288911):​n.149C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.219 in 152,192 control chromosomes in the GnomAD database, including 4,416 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 0.22 (4416 hom., cov: 32)
• Consequence: ENST00000691528.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.95

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.37 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
	ENST00000691528.2	n.149C>T		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.219 AC: 33325 AN: 152074 Hom.: 4407 Cov.: 32

Gnomad AFR AF: 0.0950

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.378

Gnomad ASJ AF: 0.216

Gnomad EAS AF: 0.215

Gnomad SAS AF: 0.331

Gnomad FIN AF: 0.185

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.257

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.219 AC: 33341 AN: 152192 Hom.: 4416 Cov.: 32 AF XY: 0.222 AC XY: 16521 AN XY: 74404

Gnomad4 AFR AF: 0.0949

Gnomad4 AMR AF: 0.378

Gnomad4 ASJ AF: 0.216

Gnomad4 EAS AF: 0.214

Gnomad4 SAS AF: 0.331

Gnomad4 FIN AF: 0.185

Gnomad4 NFE AF: 0.257

Gnomad4 OTH AF: 0.230

Alfa AF: 0.258 Hom.: 5377

Bravo AF: 0.228

Asia WGS AF: 0.279 AC: 973 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.55
DANN	Benign	0.95

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10035235; hg19: chr5-40798644;