rs11917060

Positions:

• chr3-186536644-G-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 0.21 in 152,122 control chromosomes in the GnomAD database, including 3,976 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 (3976 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.121

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.335 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: 0.210 AC: 31955 AN: 152004 Hom.: 3968 Cov.: 32

Gnomad AFR AF: 0.340

Gnomad AMI AF: 0.0505

Gnomad AMR AF: 0.204

Gnomad ASJ AF: 0.190

Gnomad EAS AF: 0.132

Gnomad SAS AF: 0.230

Gnomad FIN AF: 0.203

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.141

Gnomad OTH AF: 0.218

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

GnomAD4 genome AF: 0.210 AC: 31983 AN: 152122 Hom.: 3976 Cov.: 32 AF XY: 0.213 AC XY: 15869 AN XY: 74372

Gnomad4 AFR AF: 0.339

Gnomad4 AMR AF: 0.204

Gnomad4 ASJ AF: 0.190

Gnomad4 EAS AF: 0.131

Gnomad4 SAS AF: 0.230

Gnomad4 FIN AF: 0.203

Gnomad4 NFE AF: 0.141

Gnomad4 OTH AF: 0.217

Alfa AF: 0.185 Hom.: 441

Bravo AF: 0.215

Asia WGS AF: 0.190 AC: 661 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	3.4
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11917060; hg19: chr3-186254433;