rs4697708

chr4-10119565-T-C

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 0.327 in 152,112 control chromosomes in the GnomAD database, including 8,631 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 0.33 (8631 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.03

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.386 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.327 AC: 49774 AN: 151994 Hom.: 8623 Cov.: 33

Gnomad AFR AF: 0.215

Gnomad AMI AF: 0.265

Gnomad AMR AF: 0.354

Gnomad ASJ AF: 0.374

Gnomad EAS AF: 0.194

Gnomad SAS AF: 0.285

Gnomad FIN AF: 0.395

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.390

Gnomad OTH AF: 0.344

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

GnomAD4 genome AF: 0.327 AC: 49798 AN: 152112 Hom.: 8631 Cov.: 33 AF XY: 0.328 AC XY: 24363 AN XY: 74356

Gnomad4 AFR AF: 0.215

Gnomad4 AMR AF: 0.355

Gnomad4 ASJ AF: 0.374

Gnomad4 EAS AF: 0.194

Gnomad4 SAS AF: 0.284

Gnomad4 FIN AF: 0.395

Gnomad4 NFE AF: 0.390

Gnomad4 OTH AF: 0.342

Alfa AF: 0.359 Hom.: 1718

Bravo AF: 0.317

Asia WGS AF: 0.242 AC: 845 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.56
Dann	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4697708; hg19: chr4-10121189;