3-485540-A-G

Variant names:

• chr3-485540-A-G
• rs6442890
• ENST00000771643.1:n.108+1816A>G

Variant summary

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

The ENST00000771643.1(ENSG00000300434):​n.108+1816A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.495 in 151,776 control chromosomes in the GnomAD database, including 19,043 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 0.50 (19043 hom., cov: 31)
• Consequence: ENSG00000300434 ENST00000771643.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0570
• Publications: 3 publications found

Genes affected

ENSG00000300434 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.695 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000771643.1. 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
	ENSG00000300434	ENST00000771643.1		n.108+1816A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.495 AC: 75119 AN: 151660 Hom.: 19010 Cov.: 31

Gnomad AFR AF: 0.554

Gnomad AMI AF: 0.386

Gnomad AMR AF: 0.534

Gnomad ASJ AF: 0.504

Gnomad EAS AF: 0.715

Gnomad SAS AF: 0.498

Gnomad FIN AF: 0.442

Gnomad MID AF: 0.452

Gnomad NFE AF: 0.443

Gnomad OTH AF: 0.502

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

GnomAD4 genome AF: 0.495 AC: 75203 AN: 151776 Hom.: 19043 Cov.: 31 AF XY: 0.499 AC XY: 36992 AN XY: 74160

African (AFR) AF: 0.555 AC: 22960 AN: 41388

American (AMR) AF: 0.534 AC: 8151 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.504 AC: 1751 AN: 3472

East Asian (EAS) AF: 0.715 AC: 3682 AN: 5152

South Asian (SAS) AF: 0.498 AC: 2383 AN: 4782

European-Finnish (FIN) AF: 0.442 AC: 4638 AN: 10490

Middle Eastern (MID) AF: 0.466 AC: 136 AN: 292

European-Non Finnish (NFE) AF: 0.443 AC: 30095 AN: 67920

Other (OTH) AF: 0.500 AC: 1055 AN: 2110

Alfa AF: 0.455 Hom.: 9865

Bravo AF: 0.505

Asia WGS AF: 0.577 AC: 2001 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	9.3
DANN	Benign	0.73
PhyloP100		0.057

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: rs6442890;

hg19: chr3-527223;