rs1862176

Positions:

• chr5-140350859-G-A
• chr5-140350859-G-C
• chr5-140350859-G-T

Variant summary

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

The ENST00000520443.2(ENSG00000253965):​n.514-2319C>T 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 0.666 in 151,930 control chromosomes in the GnomAD database, including 34,077 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 0.67 (34077 hom., cov: 31)
• Consequence: ENST00000520443.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.264

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.811 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.514-2319C>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.666 AC: 101145 AN: 151812 Hom.: 34059 Cov.: 31

Gnomad AFR AF: 0.596

Gnomad AMI AF: 0.792

Gnomad AMR AF: 0.687

Gnomad ASJ AF: 0.651

Gnomad EAS AF: 0.832

Gnomad SAS AF: 0.751

Gnomad FIN AF: 0.633

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.689

Gnomad OTH AF: 0.674

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

GnomAD4 genome AF: 0.666 AC: 101220 AN: 151930 Hom.: 34077 Cov.: 31 AF XY: 0.665 AC XY: 49385 AN XY: 74244

Gnomad4 AFR AF: 0.596

Gnomad4 AMR AF: 0.687

Gnomad4 ASJ AF: 0.651

Gnomad4 EAS AF: 0.832

Gnomad4 SAS AF: 0.749

Gnomad4 FIN AF: 0.633

Gnomad4 NFE AF: 0.689

Gnomad4 OTH AF: 0.676

Alfa AF: 0.689 Hom.: 47652

Bravo AF: 0.668

Asia WGS AF: 0.769 AC: 2677 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	6.1
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1862176; hg19: chr5-139730444;