rs3809770

Variant names:

• chr17-48970234-A-G
• rs3809770

Your query was ambiguous. Multiple possible variants found:

• chr17-48970234-A-G
• chr17-48970234-A-T

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 0.371 in 152,028 control chromosomes in the GnomAD database, including 10,841 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 (10841 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07

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 (AMR) allele frequency at 95% confidence interval = 0.46 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: 0.371 AC: 56366 AN: 151910 Hom.: 10831 Cov.: 32

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.307

Gnomad AMR AF: 0.469

Gnomad ASJ AF: 0.415

Gnomad EAS AF: 0.242

Gnomad SAS AF: 0.251

Gnomad FIN AF: 0.393

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.408

Gnomad OTH AF: 0.406

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

GnomAD4 genome AF: 0.371 AC: 56413 AN: 152028 Hom.: 10841 Cov.: 32 AF XY: 0.370 AC XY: 27489 AN XY: 74296

Gnomad4 AFR AF: 0.294

Gnomad4 AMR AF: 0.469

Gnomad4 ASJ AF: 0.415

Gnomad4 EAS AF: 0.242

Gnomad4 SAS AF: 0.252

Gnomad4 FIN AF: 0.393

Gnomad4 NFE AF: 0.408

Gnomad4 OTH AF: 0.405

Alfa AF: 0.382 Hom.: 5085

Bravo AF: 0.374

Asia WGS AF: 0.265 AC: 922 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	0.79
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3809770; hg19: chr17-47047596;