rs3758653

Variant names:

• chr11-636399-T-C
• rs3758653

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 0.2 in 152,058 control chromosomes in the GnomAD database, including 3,152 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 0.20 (3152 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.90
• Publications: 60 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.342 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: 0.200 AC: 30343 AN: 151940 Hom.: 3138 Cov.: 32

Gnomad AFR AF: 0.181

Gnomad AMI AF: 0.165

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.264

Gnomad SAS AF: 0.356

Gnomad FIN AF: 0.242

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.174

Gnomad OTH AF: 0.209

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

GnomAD4 genome AF: 0.200 AC: 30401 AN: 152058 Hom.: 3152 Cov.: 32 AF XY: 0.207 AC XY: 15385 AN XY: 74346

African (AFR) AF: 0.182 AC: 7555 AN: 41488

American (AMR) AF: 0.268 AC: 4093 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.178 AC: 617 AN: 3468

East Asian (EAS) AF: 0.264 AC: 1361 AN: 5152

South Asian (SAS) AF: 0.356 AC: 1716 AN: 4820

European-Finnish (FIN) AF: 0.242 AC: 2567 AN: 10586

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.174 AC: 11824 AN: 67966

Other (OTH) AF: 0.212 AC: 447 AN: 2112

Alfa AF: 0.185 Hom.: 4045

Bravo AF: 0.198

Asia WGS AF: 0.322 AC: 1118 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	1.2
DANN	Benign	0.58
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs3758653; hg19: chr11-636399;