rs3808969

chr11-68005259-A-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 0.155 in 152,208 control chromosomes in the GnomAD database, including 1,981 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 0.16 (1981 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.720

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• 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: 0.155 AC: 23638 AN: 152090 Hom.: 1979 Cov.: 33

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.334

Gnomad AMR AF: 0.149

Gnomad ASJ AF: 0.182

Gnomad EAS AF: 0.181

Gnomad SAS AF: 0.170

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.178

Gnomad OTH AF: 0.153

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

GnomAD4 genome AF: 0.155 AC: 23648 AN: 152208 Hom.: 1981 Cov.: 33 AF XY: 0.155 AC XY: 11555 AN XY: 74408

Gnomad4 AFR AF: 0.103

Gnomad4 AMR AF: 0.149

Gnomad4 ASJ AF: 0.182

Gnomad4 EAS AF: 0.182

Gnomad4 SAS AF: 0.171

Gnomad4 FIN AF: 0.182

Gnomad4 NFE AF: 0.178

Gnomad4 OTH AF: 0.151

Alfa AF: 0.171 Hom.: 3006

Bravo AF: 0.151

Asia WGS AF: 0.156 AC: 542 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	3.3
Dann	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3808969; hg19: chr11-67772729;