rs7198427

Variant names:

• chr16-56651168-C-T
• rs7198427
• ENST00000568608.1:n.125-760C>T

Variant summary

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

The ENST00000568608.1(ENSG00000259923):​n.125-760C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.141 in 152,196 control chromosomes in the GnomAD database, including 1,600 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 0.14 (1600 hom., cov: 32)
• Consequence: ENSG00000259923 ENST00000568608.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13
• Publications: 12 publications found

Genes affected

ENSG00000259923 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.2 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.125-760C>T		intron_variant	Intron 1 of 2	5

Frequencies

GnomAD3 genomes AF: 0.141 AC: 21404 AN: 152078 Hom.: 1595 Cov.: 32

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.263

Gnomad AMR AF: 0.0811

Gnomad ASJ AF: 0.0999

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.125

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.141 AC: 21418 AN: 152196 Hom.: 1600 Cov.: 32 AF XY: 0.141 AC XY: 10488 AN XY: 74398

African (AFR) AF: 0.204 AC: 8460 AN: 41496

American (AMR) AF: 0.0809 AC: 1238 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0999 AC: 347 AN: 3472

East Asian (EAS) AF: 0.169 AC: 876 AN: 5174

South Asian (SAS) AF: 0.147 AC: 709 AN: 4824

European-Finnish (FIN) AF: 0.125 AC: 1322 AN: 10584

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.116 AC: 7913 AN: 68026

Other (OTH) AF: 0.132 AC: 279 AN: 2112

Alfa AF: 0.126 Hom.: 1609

Bravo AF: 0.139

Asia WGS AF: 0.177 AC: 613 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.49
DANN	Benign	0.34
PhyloP100		-1.1

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

Other links and lift over

dbSNP: rs7198427; hg19: chr16-56685080;