rs4693614

Variant names:

• chr4-83339368-A-G
• rs4693614

Variant summary

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

The variant allele was found at a frequency of 0.236 in 152,126 control chromosomes in the GnomAD database, including 4,377 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 0.24 (4377 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0110

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.284 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: 0.236 AC: 35923 AN: 152008 Hom.: 4373 Cov.: 32

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.265

Gnomad AMR AF: 0.291

Gnomad ASJ AF: 0.181

Gnomad EAS AF: 0.123

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.246

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.244

Gnomad OTH AF: 0.242

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

GnomAD4 genome AF: 0.236 AC: 35942 AN: 152126 Hom.: 4377 Cov.: 32 AF XY: 0.235 AC XY: 17503 AN XY: 74348

Gnomad4 AFR AF: 0.228

Gnomad4 AMR AF: 0.292

Gnomad4 ASJ AF: 0.181

Gnomad4 EAS AF: 0.123

Gnomad4 SAS AF: 0.155

Gnomad4 FIN AF: 0.246

Gnomad4 NFE AF: 0.244

Gnomad4 OTH AF: 0.240

Alfa AF: 0.240 Hom.: 9089

Bravo AF: 0.243

Asia WGS AF: 0.150 AC: 521 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.4
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4693614; hg19: chr4-84260521;