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:):

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374510	XR_001741601.2	n.823-1198C>A		intron_variant	Intron 2 of 6
LOC105374510	XR_001741602.2	n.91-1198C>A		intron_variant	Intron 1 of 5
LOC105374510	XR_925445.3	n.433-1198C>A		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286046	ENST00000652661.1	n.419-1198C>A		intron_variant	Intron 2 of 8

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 v4.3

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

Other links and lift over

dbSNP: rs4698702; hg19: chr4-18629525;