16-56649979-C-G

Variant names:

• chr16-56649979-C-G
• rs7191779
• ENST00000568608.1:n.124+975C>G

Variant summary

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

The ENST00000568608.1(ENSG00000259923):​n.124+975C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.451 in 152,128 control chromosomes in the GnomAD database, including 16,131 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 0.45 (16131 hom., cov: 34)
• Consequence: ENSG00000259923 ENST00000568608.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.800

Genes affected

ENSG00000259923 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.519 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
ENSG00000259923	ENST00000568608.1	n.124+975C>G		intron_variant	Intron 1 of 2	5

Frequencies

GnomAD3 genomes AF: 0.452 AC: 68634 AN: 152010 Hom.: 16130 Cov.: 34

Gnomad AFR AF: 0.319

Gnomad AMI AF: 0.790

Gnomad AMR AF: 0.437

Gnomad ASJ AF: 0.505

Gnomad EAS AF: 0.322

Gnomad SAS AF: 0.512

Gnomad FIN AF: 0.515

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.524

Gnomad OTH AF: 0.459

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

GnomAD4 genome AF: 0.451 AC: 68668 AN: 152128 Hom.: 16131 Cov.: 34 AF XY: 0.452 AC XY: 33639 AN XY: 74364

Gnomad4 AFR AF: 0.319

Gnomad4 AMR AF: 0.437

Gnomad4 ASJ AF: 0.505

Gnomad4 EAS AF: 0.322

Gnomad4 SAS AF: 0.511

Gnomad4 FIN AF: 0.515

Gnomad4 NFE AF: 0.524

Gnomad4 OTH AF: 0.459

Alfa AF: 0.346 Hom.: 948

Bravo AF: 0.437

Asia WGS AF: 0.406 AC: 1410 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.42
DANN	Benign	0.38

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: rs7191779; hg19: chr16-56683891;