rs4506917

Variant names:

• chr16-31336029-T-G
• rs4506917
• ENST00000777754.1:n.571-10321A>C

Variant summary

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

The ENST00000777754.1(ENSG00000289930):​n.571-10321A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.469 in 151,976 control chromosomes in the GnomAD database, including 17,288 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 0.47 (17288 hom., cov: 32)
• Consequence: ENSG00000289930 ENST00000777754.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.434
• Publications: 6 publications found

Genes affected

ENSG00000289930 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.664 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
ENSG00000289930	ENST00000777754.1	n.571-10321A>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.470 AC: 71333 AN: 151858 Hom.: 17293 Cov.: 32

Gnomad AFR AF: 0.393

Gnomad AMI AF: 0.430

Gnomad AMR AF: 0.421

Gnomad ASJ AF: 0.556

Gnomad EAS AF: 0.682

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.474

Gnomad MID AF: 0.606

Gnomad NFE AF: 0.524

Gnomad OTH AF: 0.492

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

GnomAD4 genome AF: 0.469 AC: 71335 AN: 151976 Hom.: 17288 Cov.: 32 AF XY: 0.464 AC XY: 34462 AN XY: 74272

African (AFR) AF: 0.392 AC: 16252 AN: 41430

American (AMR) AF: 0.421 AC: 6423 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.556 AC: 1928 AN: 3470

East Asian (EAS) AF: 0.683 AC: 3525 AN: 5160

South Asian (SAS) AF: 0.211 AC: 1015 AN: 4816

European-Finnish (FIN) AF: 0.474 AC: 5019 AN: 10578

Middle Eastern (MID) AF: 0.600 AC: 174 AN: 290

European-Non Finnish (NFE) AF: 0.524 AC: 35578 AN: 67948

Other (OTH) AF: 0.489 AC: 1031 AN: 2110

Alfa AF: 0.470 Hom.: 4013

Bravo AF: 0.470

Asia WGS AF: 0.430 AC: 1495 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.4
DANN	Benign	0.39
PhyloP100		0.43

Splicing

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

Other links and lift over

dbSNP: rs4506917; hg19: chr16-31347350;