17-48994121-A-G

Variant names:

• chr17-48994121-A-G
• rs1390154

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 0.624 in 151,996 control chromosomes in the GnomAD database, including 29,948 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 0.62 (29948 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0650
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.717 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: 0.624 AC: 94743 AN: 151878 Hom.: 29897 Cov.: 31

Gnomad AFR AF: 0.723

Gnomad AMI AF: 0.520

Gnomad AMR AF: 0.634

Gnomad ASJ AF: 0.554

Gnomad EAS AF: 0.655

Gnomad SAS AF: 0.563

Gnomad FIN AF: 0.573

Gnomad MID AF: 0.605

Gnomad NFE AF: 0.577

Gnomad OTH AF: 0.597

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

GnomAD4 genome AF: 0.624 AC: 94856 AN: 151996 Hom.: 29948 Cov.: 31 AF XY: 0.623 AC XY: 46265 AN XY: 74290

African (AFR) AF: 0.724 AC: 30008 AN: 41474

American (AMR) AF: 0.634 AC: 9676 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.554 AC: 1924 AN: 3470

East Asian (EAS) AF: 0.654 AC: 3383 AN: 5172

South Asian (SAS) AF: 0.564 AC: 2715 AN: 4818

European-Finnish (FIN) AF: 0.573 AC: 6037 AN: 10540

Middle Eastern (MID) AF: 0.620 AC: 181 AN: 292

European-Non Finnish (NFE) AF: 0.577 AC: 39192 AN: 67946

Other (OTH) AF: 0.600 AC: 1267 AN: 2110

Alfa AF: 0.581 Hom.: 13305

Bravo AF: 0.632

Asia WGS AF: 0.646 AC: 2249 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	9.2
DANN	Benign	0.67
PhyloP100		0.065

Splicing

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

Other links and lift over

dbSNP: rs1390154; hg19: chr17-47071483;