chr17-48970234-A-G

Variant names:

• chr17-48970234-A-G
• rs3809770

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 0.371 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
• Publications: 20 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.294 AC: 12197 AN: 41474

American (AMR) AF: 0.469 AC: 7158 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.415 AC: 1441 AN: 3472

East Asian (EAS) AF: 0.242 AC: 1248 AN: 5162

South Asian (SAS) AF: 0.252 AC: 1214 AN: 4824

European-Finnish (FIN) AF: 0.393 AC: 4152 AN: 10556

Middle Eastern (MID) AF: 0.439 AC: 129 AN: 294

European-Non Finnish (NFE) AF: 0.408 AC: 27741 AN: 67968

Other (OTH) AF: 0.405 AC: 853 AN: 2108

Alfa AF: 0.385 Hom.: 5769

Bravo AF: 0.374

Asia WGS AF: 0.265 AC: 922 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.79
DANN	Benign	0.79
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs3809770; hg19: chr17-47047596;