chr3-186838843-G-A

Variant names:

• chr3-186838843-G-A
• rs11711353

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 0.336 in 152,060 control chromosomes in the GnomAD database, including 9,640 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 0.34 (9640 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.168
• Publications: 2 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 (SAS) allele frequency at 95% confidence interval = 0.418 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.336 AC: 51076 AN: 151942 Hom.: 9636 Cov.: 32

Gnomad AFR AF: 0.175

Gnomad AMI AF: 0.221

Gnomad AMR AF: 0.349

Gnomad ASJ AF: 0.412

Gnomad EAS AF: 0.405

Gnomad SAS AF: 0.422

Gnomad FIN AF: 0.293

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.423

Gnomad OTH AF: 0.379

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

GnomAD4 genome AF: 0.336 AC: 51096 AN: 152060 Hom.: 9640 Cov.: 32 AF XY: 0.332 AC XY: 24644 AN XY: 74326

African (AFR) AF: 0.175 AC: 7243 AN: 41506

American (AMR) AF: 0.349 AC: 5325 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.412 AC: 1429 AN: 3468

East Asian (EAS) AF: 0.405 AC: 2093 AN: 5166

South Asian (SAS) AF: 0.423 AC: 2041 AN: 4820

European-Finnish (FIN) AF: 0.293 AC: 3097 AN: 10572

Middle Eastern (MID) AF: 0.514 AC: 151 AN: 294

European-Non Finnish (NFE) AF: 0.423 AC: 28716 AN: 67952

Other (OTH) AF: 0.380 AC: 799 AN: 2100

Alfa AF: 0.359 Hom.: 1341

Bravo AF: 0.330

Asia WGS AF: 0.383 AC: 1329 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	3.0
DANN	Benign	0.60
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs11711353; hg19: chr3-186556632;