rs3758640

chr11-33892881-G-Achr11-33892881-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 0.64 in 152,080 control chromosomes in the GnomAD database, including 31,198 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 0.64 (31198 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.126

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.655 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: 0.640 AC: 97212 AN: 151962 Hom.: 31184 Cov.: 32

Gnomad AFR AF: 0.650

Gnomad AMI AF: 0.736

Gnomad AMR AF: 0.583

Gnomad ASJ AF: 0.595

Gnomad EAS AF: 0.674

Gnomad SAS AF: 0.611

Gnomad FIN AF: 0.698

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.638

Gnomad OTH AF: 0.633

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

GnomAD4 genome AF: 0.640 AC: 97279 AN: 152080 Hom.: 31198 Cov.: 32 AF XY: 0.641 AC XY: 47624 AN XY: 74348

Gnomad4 AFR AF: 0.650

Gnomad4 AMR AF: 0.583

Gnomad4 ASJ AF: 0.595

Gnomad4 EAS AF: 0.674

Gnomad4 SAS AF: 0.611

Gnomad4 FIN AF: 0.698

Gnomad4 NFE AF: 0.638

Gnomad4 OTH AF: 0.629

Alfa AF: 0.631 Hom.: 39745

Bravo AF: 0.634

Asia WGS AF: 0.615 AC: 2136 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	0.51
Dann	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3758640; hg19: chr11-33914428;