rs1908252

Variant names:

• chr2-224620019-G-A
• rs1908252
• ENST00000839568.1:n.407-5456G>A

Your query was ambiguous. Multiple possible variants found:

• chr2-224620019-G-A
• chr2-224620019-G-C

Variant summary

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

The ENST00000839568.1(ENSG00000309216):​n.407-5456G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.488 in 151,922 control chromosomes in the GnomAD database, including 18,209 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 0.49 (18209 hom., cov: 33)
• Consequence: ENSG00000309216 ENST00000839568.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.53
• Publications: 3 publications found

Genes affected

ENSG00000309216 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.514 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000839568.1. 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
	ENSG00000309216	ENST00000839568.1		n.407-5456G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.488 AC: 74072 AN: 151804 Hom.: 18215 Cov.: 33

Gnomad AFR AF: 0.478

Gnomad AMI AF: 0.565

Gnomad AMR AF: 0.407

Gnomad ASJ AF: 0.504

Gnomad EAS AF: 0.374

Gnomad SAS AF: 0.483

Gnomad FIN AF: 0.490

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.519

Gnomad OTH AF: 0.493

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

GnomAD4 genome AF: 0.488 AC: 74100 AN: 151922 Hom.: 18209 Cov.: 33 AF XY: 0.482 AC XY: 35819 AN XY: 74240

African (AFR) AF: 0.478 AC: 19796 AN: 41428

American (AMR) AF: 0.408 AC: 6222 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.504 AC: 1748 AN: 3470

East Asian (EAS) AF: 0.372 AC: 1927 AN: 5174

South Asian (SAS) AF: 0.483 AC: 2328 AN: 4822

European-Finnish (FIN) AF: 0.490 AC: 5148 AN: 10504

Middle Eastern (MID) AF: 0.486 AC: 143 AN: 294

European-Non Finnish (NFE) AF: 0.519 AC: 35239 AN: 67952

Other (OTH) AF: 0.490 AC: 1034 AN: 2112

Alfa AF: 0.502 Hom.: 56100

Bravo AF: 0.478

Asia WGS AF: 0.410 AC: 1424 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.8
DANN	Benign	0.49
PhyloP100		1.5

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: rs1908252;

hg19: chr2-225484736;