rs4698036

Variant names:

• chr4-10329670-T-G
• rs4698036

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 0.211 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
• Publications: 16 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.183 AC: 7593 AN: 41486

American (AMR) AF: 0.259 AC: 3958 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.290 AC: 1006 AN: 3468

East Asian (EAS) AF: 0.157 AC: 809 AN: 5162

South Asian (SAS) AF: 0.187 AC: 904 AN: 4826

European-Finnish (FIN) AF: 0.212 AC: 2241 AN: 10590

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.219 AC: 14883 AN: 67986

Other (OTH) AF: 0.211 AC: 445 AN: 2106

Alfa AF: 0.218 Hom.: 12060

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
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs4698036; hg19: chr4-10331294;