rs154659

Variant names:

• chr16-89600929-T-C
• rs154659
• ENST00000769348.1:n.164+2374T>C

Variant summary

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

The ENST00000769348.1(ENSG00000300127):​n.164+2374T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.335 in 152,146 control chromosomes in the GnomAD database, including 9,467 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 0.33 (9467 hom., cov: 33)
• Consequence: ENSG00000300127 ENST00000769348.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.873
• Publications: 38 publications found

Genes affected

ENSG00000300127 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.491 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
ENSG00000300127	ENST00000769348.1	n.164+2374T>C		intron_variant	Intron 1 of 3
ENSG00000300127	ENST00000769349.1	n.189+2322T>C		intron_variant	Intron 1 of 3
ENSG00000300127	ENST00000769350.1	n.185+2322T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.334 AC: 50828 AN: 152030 Hom.: 9433 Cov.: 33

Gnomad AFR AF: 0.496

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.359

Gnomad ASJ AF: 0.276

Gnomad EAS AF: 0.387

Gnomad SAS AF: 0.288

Gnomad FIN AF: 0.293

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.245

Gnomad OTH AF: 0.283

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

GnomAD4 genome AF: 0.335 AC: 50930 AN: 152146 Hom.: 9467 Cov.: 33 AF XY: 0.336 AC XY: 24962 AN XY: 74386

African (AFR) AF: 0.496 AC: 20585 AN: 41484

American (AMR) AF: 0.360 AC: 5496 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.276 AC: 957 AN: 3466

East Asian (EAS) AF: 0.386 AC: 1998 AN: 5170

South Asian (SAS) AF: 0.288 AC: 1387 AN: 4820

European-Finnish (FIN) AF: 0.293 AC: 3107 AN: 10614

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.245 AC: 16632 AN: 67992

Other (OTH) AF: 0.289 AC: 610 AN: 2114

Alfa AF: 0.276 Hom.: 26766

Bravo AF: 0.351

Asia WGS AF: 0.409 AC: 1420 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.58
DANN	Benign	0.51
PhyloP100		-0.87

Splicing

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

Other links and lift over

dbSNP: rs154659; hg19: chr16-89667337;