chr5-140351647-T-C

Position:

• chr5-140351647-T-C

Variant summary

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

The ENST00000520443.2(ENSG00000253965):​n.514-3107A>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 0.413 in 152,092 control chromosomes in the GnomAD database, including 13,610 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 0.41 (13610 hom., cov: 32)
• Consequence: ENST00000520443.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.783

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.535 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
	ENST00000520443.2	n.514-3107A>G		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.413 AC: 62789 AN: 151974 Hom.: 13617 Cov.: 32

Gnomad AFR AF: 0.297

Gnomad AMI AF: 0.721

Gnomad AMR AF: 0.454

Gnomad ASJ AF: 0.448

Gnomad EAS AF: 0.552

Gnomad SAS AF: 0.483

Gnomad FIN AF: 0.364

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.459

Gnomad OTH AF: 0.443

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

GnomAD4 genome AF: 0.413 AC: 62788 AN: 152092 Hom.: 13610 Cov.: 32 AF XY: 0.411 AC XY: 30579 AN XY: 74348

Gnomad4 AFR AF: 0.297

Gnomad4 AMR AF: 0.453

Gnomad4 ASJ AF: 0.448

Gnomad4 EAS AF: 0.552

Gnomad4 SAS AF: 0.481

Gnomad4 FIN AF: 0.364

Gnomad4 NFE AF: 0.459

Gnomad4 OTH AF: 0.443

Alfa AF: 0.446 Hom.: 8220

Bravo AF: 0.419

Asia WGS AF: 0.464 AC: 1617 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	14
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6879217; hg19: chr5-139731232;