chr16-17937342-C-T

Variant names:

• chr16-17937342-C-T
• rs1019807
• ENST00000569048.5:n.406-4113G>A

Variant summary

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

The ENST00000569048.5(ENSG00000259929):​n.406-4113G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.733 in 152,086 control chromosomes in the GnomAD database, including 41,022 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 0.73 (41022 hom., cov: 32)
• Consequence: ENSG00000259929 ENST00000569048.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.24

Genes affected

ENSG00000259929 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.811 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107984893	XR_001752093.2	n.364+30201G>A		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000259929	ENST00000569048.5	n.406-4113G>A		intron_variant	Intron 3 of 3	5

Frequencies

GnomAD3 genomes AF: 0.733 AC: 111329 AN: 151968 Hom.: 40983 Cov.: 32

Gnomad AFR AF: 0.818

Gnomad AMI AF: 0.637

Gnomad AMR AF: 0.680

Gnomad ASJ AF: 0.699

Gnomad EAS AF: 0.766

Gnomad SAS AF: 0.670

Gnomad FIN AF: 0.638

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.712

Gnomad OTH AF: 0.735

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

GnomAD4 genome AF: 0.733 AC: 111421 AN: 152086 Hom.: 41022 Cov.: 32 AF XY: 0.728 AC XY: 54131 AN XY: 74342

Gnomad4 AFR AF: 0.818

Gnomad4 AMR AF: 0.679

Gnomad4 ASJ AF: 0.699

Gnomad4 EAS AF: 0.765

Gnomad4 SAS AF: 0.671

Gnomad4 FIN AF: 0.638

Gnomad4 NFE AF: 0.712

Gnomad4 OTH AF: 0.735

Alfa AF: 0.721 Hom.: 18215

Bravo AF: 0.742

Asia WGS AF: 0.720 AC: 2507 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.20
DANN	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1019807; hg19: chr16-18031199;