rs3806577

Variant names:

• chr2-205681426-T-C
• rs3806577

Your query was ambiguous. Multiple possible variants found:

• chr2-205681426-T-C
• chr2-205681426-T-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 0.375 in 152,112 control chromosomes in the GnomAD database, including 12,334 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 0.37 (12334 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.792

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.545 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: 0.375 AC: 56963 AN: 151994 Hom.: 12319 Cov.: 33

Gnomad AFR AF: 0.150

Gnomad AMI AF: 0.445

Gnomad AMR AF: 0.403

Gnomad ASJ AF: 0.355

Gnomad EAS AF: 0.460

Gnomad SAS AF: 0.562

Gnomad FIN AF: 0.579

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.454

Gnomad OTH AF: 0.375

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

GnomAD4 genome AF: 0.375 AC: 57003 AN: 152112 Hom.: 12334 Cov.: 33 AF XY: 0.384 AC XY: 28522 AN XY: 74330

Gnomad4 AFR AF: 0.150

Gnomad4 AMR AF: 0.404

Gnomad4 ASJ AF: 0.355

Gnomad4 EAS AF: 0.459

Gnomad4 SAS AF: 0.563

Gnomad4 FIN AF: 0.579

Gnomad4 NFE AF: 0.454

Gnomad4 OTH AF: 0.379

Alfa AF: 0.438 Hom.: 20512

Bravo AF: 0.350

Asia WGS AF: 0.507 AC: 1764 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	8.3
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3806577; hg19: chr2-206546150;