rs717293

Variant names:

• chr16-63524616-C-T
• rs717293
• ENST00000568932.5:n.434+6609G>A

Variant summary

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

The ENST00000568932.5(ENSG00000260658):​n.434+6609G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.581 in 151,954 control chromosomes in the GnomAD database, including 27,418 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 0.58 (27418 hom., cov: 32)
• Consequence: ENSG00000260658 ENST00000568932.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.460
• Publications: 2 publications found

Genes affected

ENSG00000260658 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.799 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105371308	XR_001752232.2	n.434+6609G>A		intron_variant	Intron 2 of 5
LOC105371308	XR_007065220.1	n.434+6609G>A		intron_variant	Intron 2 of 3
LOC105371308	XR_007065221.1	n.434+6609G>A		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000260658	ENST00000568932.5	n.434+6609G>A		intron_variant	Intron 2 of 3	5
ENSG00000260658	ENST00000655786.3	n.436-2838G>A		intron_variant	Intron 2 of 2
ENSG00000260658	ENST00000665929.2	n.438+6609G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.581 AC: 88232 AN: 151836 Hom.: 27376 Cov.: 32

Gnomad AFR AF: 0.806

Gnomad AMI AF: 0.399

Gnomad AMR AF: 0.478

Gnomad ASJ AF: 0.528

Gnomad EAS AF: 0.622

Gnomad SAS AF: 0.446

Gnomad FIN AF: 0.360

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.512

Gnomad OTH AF: 0.617

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

GnomAD4 genome AF: 0.581 AC: 88312 AN: 151954 Hom.: 27418 Cov.: 32 AF XY: 0.569 AC XY: 42227 AN XY: 74256

African (AFR) AF: 0.806 AC: 33420 AN: 41452

American (AMR) AF: 0.477 AC: 7274 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.528 AC: 1831 AN: 3468

East Asian (EAS) AF: 0.621 AC: 3182 AN: 5124

South Asian (SAS) AF: 0.445 AC: 2139 AN: 4812

European-Finnish (FIN) AF: 0.360 AC: 3801 AN: 10548

Middle Eastern (MID) AF: 0.558 AC: 164 AN: 294

European-Non Finnish (NFE) AF: 0.512 AC: 34824 AN: 67980

Other (OTH) AF: 0.621 AC: 1313 AN: 2114

Alfa AF: 0.536 Hom.: 37144

Bravo AF: 0.602

Asia WGS AF: 0.579 AC: 2011 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.2
DANN	Benign	0.42
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs717293; hg19: chr16-63558520;