3-163030564-C-G

Variant names:

• chr3-163030564-C-G
• rs4260465
• ENST00000490357.1:n.103+4066C>G

Variant summary

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

The ENST00000490357.1(ENSG00000241168):​n.103+4066C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.347 in 151,450 control chromosomes in the GnomAD database, including 9,413 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 0.35 (9413 hom., cov: 32)
• Consequence: ENSG00000241168 ENST00000490357.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.421
• Publications: 5 publications found

Genes affected

ENSG00000241168 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.505 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000490357.1. 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
	ENSG00000241168	ENST00000490357.1	TSL:5	n.103+4066C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.347 AC: 52449 AN: 151334 Hom.: 9402 Cov.: 32

Gnomad AFR AF: 0.388

Gnomad AMI AF: 0.234

Gnomad AMR AF: 0.384

Gnomad ASJ AF: 0.388

Gnomad EAS AF: 0.523

Gnomad SAS AF: 0.282

Gnomad FIN AF: 0.230

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.320

Gnomad OTH AF: 0.394

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

GnomAD4 genome AF: 0.347 AC: 52478 AN: 151450 Hom.: 9413 Cov.: 32 AF XY: 0.342 AC XY: 25308 AN XY: 73978

African (AFR) AF: 0.388 AC: 16044 AN: 41364

American (AMR) AF: 0.383 AC: 5797 AN: 15128

Ashkenazi Jewish (ASJ) AF: 0.388 AC: 1343 AN: 3464

East Asian (EAS) AF: 0.522 AC: 2684 AN: 5144

South Asian (SAS) AF: 0.282 AC: 1362 AN: 4826

European-Finnish (FIN) AF: 0.230 AC: 2424 AN: 10540

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.320 AC: 21668 AN: 67672

Other (OTH) AF: 0.391 AC: 824 AN: 2106

Alfa AF: 0.167 Hom.: 283

Bravo AF: 0.364

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.19
DANN	Benign	0.34
PhyloP100		-0.42

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: rs4260465;

hg19: chr3-162748352;