rs4618379

Variant names:

• chr4-69049206-T-C
• rs4618379
• ENST00000766642.1:n.52-2087A>G

Variant summary

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

The ENST00000766642.1(ENSG00000299813):​n.52-2087A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.201 in 152,014 control chromosomes in the GnomAD database, including 3,232 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 0.20 (3232 hom., cov: 32)
• Consequence: ENSG00000299813 ENST00000766642.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.688
• Publications: 1 publications found

Genes affected

ENSG00000299813 (HGNC:58801):

LOC105377265 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.249 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000766642.1. 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
	ENSG00000299813	ENST00000766642.1		n.52-2087A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.201 AC: 30571 AN: 151896 Hom.: 3231 Cov.: 32

Gnomad AFR AF: 0.253

Gnomad AMI AF: 0.271

Gnomad AMR AF: 0.167

Gnomad ASJ AF: 0.200

Gnomad EAS AF: 0.174

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.205

Gnomad MID AF: 0.183

Gnomad NFE AF: 0.177

Gnomad OTH AF: 0.196

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

GnomAD4 genome AF: 0.201 AC: 30588 AN: 152014 Hom.: 3232 Cov.: 32 AF XY: 0.201 AC XY: 14905 AN XY: 74312

African (AFR) AF: 0.253 AC: 10507 AN: 41496

American (AMR) AF: 0.167 AC: 2545 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.200 AC: 694 AN: 3470

East Asian (EAS) AF: 0.174 AC: 902 AN: 5184

South Asian (SAS) AF: 0.223 AC: 1075 AN: 4820

European-Finnish (FIN) AF: 0.205 AC: 2163 AN: 10576

Middle Eastern (MID) AF: 0.186 AC: 54 AN: 290

European-Non Finnish (NFE) AF: 0.177 AC: 11987 AN: 67876

Other (OTH) AF: 0.197 AC: 414 AN: 2106

Alfa AF: 0.181 Hom.: 339

Bravo AF: 0.198

Asia WGS AF: 0.190 AC: 656 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.89
DANN	Benign	0.59
PhyloP100		-0.69

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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: rs4618379;

hg19: chr4-69914924;