rs16864755

Variant names:

• chr2-223409904-G-A
• rs16864755
• ENST00000797088.1:n.295-11338C>T

Variant summary

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

The ENST00000797088.1(ENSG00000303770):​n.295-11338C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0775 in 152,048 control chromosomes in the GnomAD database, including 587 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 0.077 (587 hom., cov: 32)
• Consequence: ENSG00000303770 ENST00000797088.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23
• Publications: 9 publications found

Genes affected

ENSG00000303770 (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 (AMR) allele frequency at 95% confidence interval = 0.0886 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000797088.1. 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
	ENSG00000303770	ENST00000797088.1		n.295-11338C>T		intron	N/A
	ENSG00000303770	ENST00000797089.1		n.149-11338C>T		intron	N/A
	ENSG00000303770	ENST00000797092.1		n.84-11338C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0775 AC: 11782 AN: 151930 Hom.: 587 Cov.: 32

Gnomad AFR AF: 0.0434

Gnomad AMI AF: 0.0714

Gnomad AMR AF: 0.0914

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.00482

Gnomad SAS AF: 0.0414

Gnomad FIN AF: 0.115

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.0905

Gnomad OTH AF: 0.0928

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

GnomAD4 genome AF: 0.0775 AC: 11783 AN: 152048 Hom.: 587 Cov.: 32 AF XY: 0.0783 AC XY: 5819 AN XY: 74334

African (AFR) AF: 0.0433 AC: 1797 AN: 41486

American (AMR) AF: 0.0913 AC: 1393 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.202 AC: 700 AN: 3468

East Asian (EAS) AF: 0.00483 AC: 25 AN: 5172

South Asian (SAS) AF: 0.0415 AC: 200 AN: 4824

European-Finnish (FIN) AF: 0.115 AC: 1215 AN: 10562

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.0905 AC: 6148 AN: 67956

Other (OTH) AF: 0.0928 AC: 196 AN: 2112

Alfa AF: 0.0855 Hom.: 2226

Bravo AF: 0.0735

Asia WGS AF: 0.0380 AC: 130 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	0.76
DANN	Benign	0.74
PhyloP100		-1.2

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: rs16864755;

hg19: chr2-224274622;