chr5-87909191-T-C

Position:

• chr5-87909191-T-C

Variant summary

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

The ENST00000668454.1(ENSG00000287862):​n.219-41312A>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 0.131 in 152,112 control chromosomes in the GnomAD database, including 2,773 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 0.13 (2773 hom., cov: 32)
• Consequence: ENST00000668454.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.730

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.351 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000668454.1	n.219-41312A>G		intron_variant, non_coding_transcript_variant
	ENST00000655360.1	n.388-41315A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.131 AC: 19844 AN: 151994 Hom.: 2764 Cov.: 32

Gnomad AFR AF: 0.356

Gnomad AMI AF: 0.0724

Gnomad AMR AF: 0.0894

Gnomad ASJ AF: 0.0130

Gnomad EAS AF: 0.00443

Gnomad SAS AF: 0.0423

Gnomad FIN AF: 0.0445

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0398

Gnomad OTH AF: 0.0942

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

GnomAD4 genome AF: 0.131 AC: 19880 AN: 152112 Hom.: 2773 Cov.: 32 AF XY: 0.127 AC XY: 9425 AN XY: 74386

Gnomad4 AFR AF: 0.356

Gnomad4 AMR AF: 0.0891

Gnomad4 ASJ AF: 0.0130

Gnomad4 EAS AF: 0.00444

Gnomad4 SAS AF: 0.0419

Gnomad4 FIN AF: 0.0445

Gnomad4 NFE AF: 0.0398

Gnomad4 OTH AF: 0.0960

Alfa AF: 0.0934 Hom.: 215

Bravo AF: 0.143

Asia WGS AF: 0.0570 AC: 197 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.29
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1358572; hg19: chr5-87205008;