chr17-30188461-A-G

Variant names:

• chr17-30188461-A-G
• rs1906451

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 0.388 in 151,858 control chromosomes in the GnomAD database, including 13,657 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 0.39 (13657 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.47
• Publications: 16 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.795 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: 0.388 AC: 58913 AN: 151740 Hom.: 13662 Cov.: 29

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.470

Gnomad AMR AF: 0.498

Gnomad ASJ AF: 0.547

Gnomad EAS AF: 0.814

Gnomad SAS AF: 0.532

Gnomad FIN AF: 0.439

Gnomad MID AF: 0.455

Gnomad NFE AF: 0.451

Gnomad OTH AF: 0.431

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

GnomAD4 genome AF: 0.388 AC: 58896 AN: 151858 Hom.: 13657 Cov.: 29 AF XY: 0.397 AC XY: 29482 AN XY: 74208

African (AFR) AF: 0.144 AC: 5981 AN: 41468

American (AMR) AF: 0.497 AC: 7574 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.547 AC: 1900 AN: 3472

East Asian (EAS) AF: 0.816 AC: 4205 AN: 5156

South Asian (SAS) AF: 0.531 AC: 2557 AN: 4816

European-Finnish (FIN) AF: 0.439 AC: 4609 AN: 10510

Middle Eastern (MID) AF: 0.441 AC: 128 AN: 290

European-Non Finnish (NFE) AF: 0.451 AC: 30615 AN: 67902

Other (OTH) AF: 0.428 AC: 901 AN: 2106

Alfa AF: 0.404 Hom.: 11253

Bravo AF: 0.386

Asia WGS AF: 0.577 AC: 2005 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.1
DANN	Benign	0.61
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs1906451; hg19: chr17-28515479;