rs4698702

Positions:

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

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000652661.1(ENSG00000286046):​n.419-1198C>A variant causes a intron, non coding transcript 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: ENST00000652661.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.254

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC105374510	XR_001741602.2	n.91-1198C>A		intron_variant, non_coding_transcript_variant
LOC105374510	XR_001741601.2	n.823-1198C>A		intron_variant, non_coding_transcript_variant
LOC105374510	XR_925445.3	n.433-1198C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000652661.1	n.419-1198C>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.126

Gnomad4 AMR AF: 0.375

Gnomad4 ASJ AF: 0.202

Gnomad4 EAS AF: 0.433

Gnomad4 SAS AF: 0.301

Gnomad4 FIN AF: 0.140

Gnomad4 NFE AF: 0.168

Gnomad4 OTH AF: 0.180

Alfa AF: 0.175 Hom.: 3748

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

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs4698702; hg19: chr4-18629525;