rs4698036

Positions:

• chr4-10329670-T-G

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 0.211 in 152,092 control chromosomes in the GnomAD database, including 3,390 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 0.21 (3390 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.57

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.253 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.211 AC: 32033 AN: 151974 Hom.: 3383 Cov.: 32

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.157

Gnomad AMR AF: 0.259

Gnomad ASJ AF: 0.290

Gnomad EAS AF: 0.157

Gnomad SAS AF: 0.187

Gnomad FIN AF: 0.212

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.219

Gnomad OTH AF: 0.214

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

GnomAD4 genome AF: 0.211 AC: 32061 AN: 152092 Hom.: 3390 Cov.: 32 AF XY: 0.211 AC XY: 15658 AN XY: 74328

Gnomad4 AFR AF: 0.183

Gnomad4 AMR AF: 0.259

Gnomad4 ASJ AF: 0.290

Gnomad4 EAS AF: 0.157

Gnomad4 SAS AF: 0.187

Gnomad4 FIN AF: 0.212

Gnomad4 NFE AF: 0.219

Gnomad4 OTH AF: 0.211

Alfa AF: 0.221 Hom.: 5086

Bravo AF: 0.214

Asia WGS AF: 0.174 AC: 605 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.26
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4698036; hg19: chr4-10331294;