5-88019435-T-C

Variant names:

• chr5-88019435-T-C
• rs965566
• ENST00000655360.1:n.387+28154A>G

Variant summary

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

The ENST00000655360.1(ENSG00000287862):​n.387+28154A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.553 in 152,066 control chromosomes in the GnomAD database, including 26,604 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 0.55 (26604 hom., cov: 32)
• Consequence: ENSG00000287862 ENST00000655360.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.00

Genes affected

ENSG00000287862 (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 (EAS) allele frequency at 95% confidence interval = 0.755 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287862	ENST00000655360.1	n.387+28154A>G		intron_variant	Intron 2 of 2
ENSG00000287862	ENST00000668454.1	n.218+28154A>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.554 AC: 84143 AN: 151948 Hom.: 26611 Cov.: 32

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.783

Gnomad AMR AF: 0.619

Gnomad ASJ AF: 0.559

Gnomad EAS AF: 0.776

Gnomad SAS AF: 0.589

Gnomad FIN AF: 0.718

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.692

Gnomad OTH AF: 0.565

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

GnomAD4 genome AF: 0.553 AC: 84136 AN: 152066 Hom.: 26604 Cov.: 32 AF XY: 0.557 AC XY: 41406 AN XY: 74314

Gnomad4 AFR AF: 0.223

Gnomad4 AMR AF: 0.619

Gnomad4 ASJ AF: 0.559

Gnomad4 EAS AF: 0.775

Gnomad4 SAS AF: 0.588

Gnomad4 FIN AF: 0.718

Gnomad4 NFE AF: 0.692

Gnomad4 OTH AF: 0.561

Alfa AF: 0.663 Hom.: 52260

Bravo AF: 0.533

Asia WGS AF: 0.633 AC: 2198 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.9
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs965566; hg19: chr5-87315252;