rs2102808

Variant names:

• chr2-168260515-G-T
• rs2102808
• ENST00000816341.1:n.109-4581G>T

Variant summary

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

The ENST00000816341.1(ENSG00000306224):​n.109-4581G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.156 in 152,234 control chromosomes in the GnomAD database, including 1,988 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 0.16 (1988 hom., cov: 33)
• Consequence: ENSG00000306224 ENST00000816341.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.241
• Publications: 38 publications found

Genes affected

ENSG00000306224 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.303 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000816341.1. 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
	ENSG00000306224	ENST00000816341.1		n.109-4581G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.156 AC: 23723 AN: 152114 Hom.: 1984 Cov.: 33

Gnomad AFR AF: 0.188

Gnomad AMI AF: 0.0352

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.315

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.0962

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.168

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

GnomAD4 genome AF: 0.156 AC: 23747 AN: 152234 Hom.: 1988 Cov.: 33 AF XY: 0.155 AC XY: 11525 AN XY: 74428

African (AFR) AF: 0.188 AC: 7823 AN: 41538

American (AMR) AF: 0.195 AC: 2983 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.103 AC: 357 AN: 3472

East Asian (EAS) AF: 0.316 AC: 1634 AN: 5178

South Asian (SAS) AF: 0.194 AC: 933 AN: 4820

European-Finnish (FIN) AF: 0.0962 AC: 1021 AN: 10610

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.126 AC: 8540 AN: 68012

Other (OTH) AF: 0.170 AC: 359 AN: 2112

Alfa AF: 0.0211 Hom.: 198

Bravo AF: 0.166

Asia WGS AF: 0.236 AC: 823 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.1
DANN	Benign	0.56
PhyloP100		0.24

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: rs2102808;

hg19: chr2-169117025;