rs16954462

Variant names:

• chr13-87399205-G-A
• rs16954462
• ENST00000835138.1:n.604-24291G>A

Variant summary

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

The ENST00000835138.1(ENSG00000285699):​n.604-24291G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0379 in 152,154 control chromosomes in the GnomAD database, including 200 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 0.038 (200 hom., cov: 32)
• Consequence: ENSG00000285699 ENST00000835138.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0120
• Publications: 0 publications found

Genes affected

ENSG00000285699 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0902 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000835138.1. 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
	ENSG00000285699	ENST00000835138.1		n.604-24291G>A		intron	N/A
	ENSG00000285699	ENST00000835139.1		n.101-24291G>A		intron	N/A
	ENSG00000285699	ENST00000835140.1		n.80-24291G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0378 AC: 5750 AN: 152036 Hom.: 199 Cov.: 32

Gnomad AFR AF: 0.0923

Gnomad AMI AF: 0.0154

Gnomad AMR AF: 0.0296

Gnomad ASJ AF: 0.0337

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0178

Gnomad FIN AF: 0.00434

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0166

Gnomad OTH AF: 0.0378

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

GnomAD4 genome AF: 0.0379 AC: 5770 AN: 152154 Hom.: 200 Cov.: 32 AF XY: 0.0376 AC XY: 2801 AN XY: 74396

African (AFR) AF: 0.0926 AC: 3844 AN: 41504

American (AMR) AF: 0.0294 AC: 448 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.0337 AC: 117 AN: 3470

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5168

South Asian (SAS) AF: 0.0174 AC: 84 AN: 4830

European-Finnish (FIN) AF: 0.00434 AC: 46 AN: 10596

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0166 AC: 1130 AN: 68022

Other (OTH) AF: 0.0374 AC: 79 AN: 2114

Alfa AF: 0.0236 Hom.: 160

Bravo AF: 0.0422

Asia WGS AF: 0.0140 AC: 50 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.4
DANN	Benign	0.40
PhyloP100		-0.012

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: rs16954462;

hg19: chr13-88051460;