rs16837190

Variant names:

• chr1-238598126-G-A
• rs16837190
• ENST00000716151.1:n.548-19015G>A

Variant summary

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

The ENST00000716151.1(ENSG00000234464):​n.548-19015G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0459 in 152,126 control chromosomes in the GnomAD database, including 219 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 0.046 (219 hom., cov: 32)
• Consequence: ENSG00000234464 ENST00000716151.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.82
• Publications: 2 publications found

Genes affected

ENSG00000234464 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.12 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000716151.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000234464	ENST00000716151.1		n.548-19015G>A		intron	N/A
	ENSG00000234464	ENST00000716155.1		n.473-15357G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0459 AC: 6981 AN: 152008 Hom.: 219 Cov.: 32

Gnomad AFR AF: 0.00990

Gnomad AMI AF: 0.132

Gnomad AMR AF: 0.0426

Gnomad ASJ AF: 0.0579

Gnomad EAS AF: 0.128

Gnomad SAS AF: 0.0798

Gnomad FIN AF: 0.0850

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0517

Gnomad OTH AF: 0.0545

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

GnomAD4 genome AF: 0.0459 AC: 6981 AN: 152126 Hom.: 219 Cov.: 32 AF XY: 0.0479 AC XY: 3558 AN XY: 74338

African (AFR) AF: 0.00990 AC: 411 AN: 41516

American (AMR) AF: 0.0425 AC: 650 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0579 AC: 201 AN: 3470

East Asian (EAS) AF: 0.128 AC: 657 AN: 5144

South Asian (SAS) AF: 0.0803 AC: 387 AN: 4820

European-Finnish (FIN) AF: 0.0850 AC: 900 AN: 10584

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0517 AC: 3515 AN: 67986

Other (OTH) AF: 0.0544 AC: 115 AN: 2114

Alfa AF: 0.0419 Hom.: 101

Bravo AF: 0.0430

Asia WGS AF: 0.0930 AC: 327 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.3
DANN	Benign	0.58
PhyloP100		1.8

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs16837190;

hg19: chr1-238761426;