rs11568835

Variant names:

• chr4-109911514-G-A
• rs11568835

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 0.0295 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
• Publications: 12 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.0282 AC: 1170 AN: 41538

American (AMR) AF: 0.118 AC: 1801 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.00519 AC: 18 AN: 3470

East Asian (EAS) AF: 0.185 AC: 959 AN: 5176

South Asian (SAS) AF: 0.0635 AC: 306 AN: 4820

European-Finnish (FIN) AF: 0.00510 AC: 54 AN: 10598

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.00169 AC: 115 AN: 68020

Other (OTH) AF: 0.0275 AC: 58 AN: 2112

Alfa AF: 0.0288 Hom.: 127

Bravo AF: 0.0404

Asia WGS AF: 0.142 AC: 496 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.027
DANN	Benign	0.61
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs11568835; hg19: chr4-110832670;