rs4888535

Variant names:

• chr16-76727759-T-A
• rs4888535
• ENST00000563764.2:n.*123-91827T>A

Your query was ambiguous. Multiple possible variants found:

• chr16-76727759-T-A
• chr16-76727759-T-C
• chr16-76727759-T-G

Variant summary

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

The ENST00000563764.2(ENSG00000287694):​n.*123-91827T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.33 in 151,886 control chromosomes in the GnomAD database, including 8,466 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 0.33 (8466 hom., cov: 32)
• Consequence: ENSG00000287694 ENST00000563764.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.902

Genes affected

ENSG00000287694 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.388 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
ENSG00000287694	ENST00000563764.2	n.*123-91827T>A		intron_variant	Intron 3 of 3	3		ENSP00000455258.1

Frequencies

GnomAD3 genomes AF: 0.330 AC: 50069 AN: 151768 Hom.: 8464 Cov.: 32

Gnomad AFR AF: 0.305

Gnomad AMI AF: 0.281

Gnomad AMR AF: 0.396

Gnomad ASJ AF: 0.343

Gnomad EAS AF: 0.381

Gnomad SAS AF: 0.363

Gnomad FIN AF: 0.281

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.331

Gnomad OTH AF: 0.340

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

GnomAD4 genome AF: 0.330 AC: 50092 AN: 151886 Hom.: 8466 Cov.: 32 AF XY: 0.330 AC XY: 24511 AN XY: 74204

Gnomad4 AFR AF: 0.305

Gnomad4 AMR AF: 0.396

Gnomad4 ASJ AF: 0.343

Gnomad4 EAS AF: 0.381

Gnomad4 SAS AF: 0.361

Gnomad4 FIN AF: 0.281

Gnomad4 NFE AF: 0.331

Gnomad4 OTH AF: 0.337

Alfa AF: 0.331 Hom.: 1038

Bravo AF: 0.335

Asia WGS AF: 0.364 AC: 1258 AN: 3450

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	6.9
DANN	Benign	0.79

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs4888535; hg19: chr16-76761656;