rs258595

Variant names:

• chr16-55235276-G-A
• rs258595
• ENST00000761294.1:n.244-442C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000761294.1(ENSG00000299155):​n.244-442C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.667 in 150,702 control chromosomes in the GnomAD database, including 33,752 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 (33752 hom., cov: 28)
• Consequence: ENSG00000299155 ENST00000761294.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0100
• Publications: 0 publications found

Genes affected

ENSG00000299155 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 = 0.806 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
ENSG00000299155	ENST00000761294.1	n.244-442C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.667 AC: 100499 AN: 150598 Hom.: 33741 Cov.: 28

Gnomad AFR AF: 0.631

Gnomad AMI AF: 0.689

Gnomad AMR AF: 0.689

Gnomad ASJ AF: 0.712

Gnomad EAS AF: 0.826

Gnomad SAS AF: 0.805

Gnomad FIN AF: 0.683

Gnomad MID AF: 0.787

Gnomad NFE AF: 0.657

Gnomad OTH AF: 0.676

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

GnomAD4 genome AF: 0.667 AC: 100561 AN: 150702 Hom.: 33752 Cov.: 28 AF XY: 0.670 AC XY: 49286 AN XY: 73542

African (AFR) AF: 0.631 AC: 26003 AN: 41200

American (AMR) AF: 0.689 AC: 10420 AN: 15124

Ashkenazi Jewish (ASJ) AF: 0.712 AC: 2461 AN: 3456

East Asian (EAS) AF: 0.827 AC: 4244 AN: 5134

South Asian (SAS) AF: 0.806 AC: 3856 AN: 4786

European-Finnish (FIN) AF: 0.683 AC: 6847 AN: 10018

Middle Eastern (MID) AF: 0.779 AC: 226 AN: 290

European-Non Finnish (NFE) AF: 0.657 AC: 44468 AN: 67692

Other (OTH) AF: 0.674 AC: 1409 AN: 2092

Alfa AF: 0.663 Hom.: 4161

Bravo AF: 0.668

Asia WGS AF: 0.785 AC: 2704 AN: 3444

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.7
DANN	Benign	0.33
PhyloP100		-0.010

Splicing

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

Other links and lift over

dbSNP: rs258595; hg19: chr16-55269188;