rs4698702

Variant names:

• chr4-18627902-C-A
• rs4698702
• ENST00000652661.1:n.419-1198C>A

Your query was ambiguous. Multiple possible variants found:

• chr4-18627902-C-A
• chr4-18627902-C-G

Variant summary

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

The ENST00000652661.1(ENSG00000286046):​n.419-1198C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.189 in 152,200 control chromosomes in the GnomAD database, including 3,446 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 0.19 (3446 hom., cov: 33)
• Consequence: ENSG00000286046 ENST00000652661.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.254
• Publications: 2 publications found

Genes affected

ENSG00000286046 (HGNC:59078):

LOC105374510 (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 = 0.418 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000652661.1. 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
	ENSG00000286046	ENST00000652661.1		n.419-1198C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.189 AC: 28796 AN: 152082 Hom.: 3431 Cov.: 33

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.162

Gnomad AMR AF: 0.374

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.433

Gnomad SAS AF: 0.300

Gnomad FIN AF: 0.140

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.180

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

GnomAD4 genome AF: 0.189 AC: 28826 AN: 152200 Hom.: 3446 Cov.: 33 AF XY: 0.195 AC XY: 14476 AN XY: 74418

African (AFR) AF: 0.126 AC: 5243 AN: 41540

American (AMR) AF: 0.375 AC: 5728 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.202 AC: 701 AN: 3464

East Asian (EAS) AF: 0.433 AC: 2238 AN: 5174

South Asian (SAS) AF: 0.301 AC: 1447 AN: 4814

European-Finnish (FIN) AF: 0.140 AC: 1481 AN: 10592

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.168 AC: 11422 AN: 68010

Other (OTH) AF: 0.180 AC: 381 AN: 2116

Alfa AF: 0.182 Hom.: 5655

Bravo AF: 0.208

Asia WGS AF: 0.333 AC: 1156 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	9.2
DANN	Benign	0.72
PhyloP100		-0.25

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: rs4698702;

hg19: chr4-18629525;