rs4698014

Variant names:

• chr4-10284677-C-T
• rs4698014

Variant summary

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

The variant allele was found at a frequency of 0.181 in 151,926 control chromosomes in the GnomAD database, including 2,657 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 0.18 (2657 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.29
• Publications: 15 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.24 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.181 AC: 27549 AN: 151808 Hom.: 2651 Cov.: 32

Gnomad AFR AF: 0.0996

Gnomad AMI AF: 0.156

Gnomad AMR AF: 0.246

Gnomad ASJ AF: 0.276

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.180

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.213

Gnomad OTH AF: 0.189

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

GnomAD4 genome AF: 0.181 AC: 27556 AN: 151926 Hom.: 2657 Cov.: 32 AF XY: 0.182 AC XY: 13496 AN XY: 74240

African (AFR) AF: 0.0994 AC: 4123 AN: 41472

American (AMR) AF: 0.247 AC: 3765 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.276 AC: 956 AN: 3466

East Asian (EAS) AF: 0.138 AC: 711 AN: 5168

South Asian (SAS) AF: 0.180 AC: 865 AN: 4806

European-Finnish (FIN) AF: 0.197 AC: 2073 AN: 10514

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.213 AC: 14463 AN: 67932

Other (OTH) AF: 0.187 AC: 392 AN: 2096

Alfa AF: 0.201 Hom.: 5955

Bravo AF: 0.181

Asia WGS AF: 0.146 AC: 505 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.64
DANN	Benign	0.36
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs4698014; hg19: chr4-10286301;