rs4489285

Variant names:

• chr8-31540605-G-A
• rs4489285
• ENST00000656443.1:n.212+449G>A

Your query was ambiguous. Multiple possible variants found:

• chr8-31540605-G-A
• chr8-31540605-G-C
• chr8-31540605-G-T

Variant summary

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

The ENST00000656443.1(ENSG00000287204):​n.212+449G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.585 in 151,952 control chromosomes in the GnomAD database, including 26,237 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 0.58 (26237 hom., cov: 32)
• Consequence: ENSG00000287204 ENST00000656443.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.04
• Publications: 3 publications found

Genes affected

ENSG00000287204 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.792 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000656443.1. 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
	ENSG00000287204	ENST00000656443.1		n.212+449G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.585 AC: 88783 AN: 151834 Hom.: 26212 Cov.: 32

Gnomad AFR AF: 0.608

Gnomad AMI AF: 0.536

Gnomad AMR AF: 0.504

Gnomad ASJ AF: 0.673

Gnomad EAS AF: 0.812

Gnomad SAS AF: 0.606

Gnomad FIN AF: 0.547

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.571

Gnomad OTH AF: 0.616

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

GnomAD4 genome AF: 0.585 AC: 88851 AN: 151952 Hom.: 26237 Cov.: 32 AF XY: 0.581 AC XY: 43147 AN XY: 74264

African (AFR) AF: 0.607 AC: 25157 AN: 41418

American (AMR) AF: 0.504 AC: 7681 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.673 AC: 2332 AN: 3466

East Asian (EAS) AF: 0.812 AC: 4194 AN: 5164

South Asian (SAS) AF: 0.608 AC: 2932 AN: 4820

European-Finnish (FIN) AF: 0.547 AC: 5774 AN: 10564

Middle Eastern (MID) AF: 0.735 AC: 216 AN: 294

European-Non Finnish (NFE) AF: 0.571 AC: 38775 AN: 67954

Other (OTH) AF: 0.618 AC: 1302 AN: 2108

Alfa AF: 0.578 Hom.: 71444

Bravo AF: 0.583

Asia WGS AF: 0.685 AC: 2378 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	8.2
DANN	Benign	0.65
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: rs4489285;

hg19: chr8-31398121;