rs16861690

Variant names:

• chr2-173441809-A-G
• rs16861690
• ENST00000841881.1:n.306-1445T>C

Variant summary

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

The ENST00000841881.1(ENSG00000309536):​n.306-1445T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.153 in 152,164 control chromosomes in the GnomAD database, including 2,899 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 0.15 (2899 hom., cov: 33)
• Consequence: ENSG00000309536 ENST00000841881.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00
• Publications: 0 publications found

Genes affected

ENSG00000309536 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.347 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000841881.1. 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
	ENSG00000309536	ENST00000841881.1		n.306-1445T>C		intron	N/A
	ENSG00000309536	ENST00000841882.1		n.99-1445T>C		intron	N/A
	ENSG00000309536	ENST00000841883.1		n.69-1445T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.153 AC: 23195 AN: 152046 Hom.: 2895 Cov.: 33

Gnomad AFR AF: 0.321

Gnomad AMI AF: 0.0463

Gnomad AMR AF: 0.119

Gnomad ASJ AF: 0.0879

Gnomad EAS AF: 0.361

Gnomad SAS AF: 0.230

Gnomad FIN AF: 0.0567

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0563

Gnomad OTH AF: 0.150

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

GnomAD4 genome AF: 0.153 AC: 23223 AN: 152164 Hom.: 2899 Cov.: 33 AF XY: 0.153 AC XY: 11362 AN XY: 74400

African (AFR) AF: 0.321 AC: 13316 AN: 41482

American (AMR) AF: 0.119 AC: 1822 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0879 AC: 305 AN: 3468

East Asian (EAS) AF: 0.360 AC: 1863 AN: 5172

South Asian (SAS) AF: 0.228 AC: 1099 AN: 4818

European-Finnish (FIN) AF: 0.0567 AC: 601 AN: 10606

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.0563 AC: 3828 AN: 68004

Other (OTH) AF: 0.151 AC: 319 AN: 2114

Alfa AF: 0.0896 Hom.: 4728

Bravo AF: 0.163

Asia WGS AF: 0.298 AC: 1032 AN: 3454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.18
DANN	Benign	0.19
PhyloP100		-1.0

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: rs16861690;

hg19: chr2-174306537;