rs11568835

chr4-109911514-G-A

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 0.0295 in 152,218 control chromosomes in the GnomAD database, including 260 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 0.029 (260 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.35

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.176 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: 0.0294 AC: 4468 AN: 152100 Hom.: 256 Cov.: 32

Gnomad AFR AF: 0.0281

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.00519

Gnomad EAS AF: 0.185

Gnomad SAS AF: 0.0636

Gnomad FIN AF: 0.00510

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.00169

Gnomad OTH AF: 0.0263

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

GnomAD4 genome AF: 0.0295 AC: 4485 AN: 152218 Hom.: 260 Cov.: 32 AF XY: 0.0330 AC XY: 2455 AN XY: 74412

Gnomad4 AFR AF: 0.0282

Gnomad4 AMR AF: 0.118

Gnomad4 ASJ AF: 0.00519

Gnomad4 EAS AF: 0.185

Gnomad4 SAS AF: 0.0635

Gnomad4 FIN AF: 0.00510

Gnomad4 NFE AF: 0.00169

Gnomad4 OTH AF: 0.0275

Alfa AF: 0.0306 Hom.: 119

Bravo AF: 0.0404

Asia WGS AF: 0.142 AC: 496 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.027
Dann	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11568835; hg19: chr4-110832670;