17-48994121-A-G

Variant names:

• chr17-48994121-A-G
• rs1390154

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 0.624 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.624 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

Gnomad4 AFR AF: 0.724

Gnomad4 AMR AF: 0.634

Gnomad4 ASJ AF: 0.554

Gnomad4 EAS AF: 0.654

Gnomad4 SAS AF: 0.564

Gnomad4 FIN AF: 0.573

Gnomad4 NFE AF: 0.577

Gnomad4 OTH AF: 0.600

Alfa AF: 0.586 Hom.: 8354

Bravo AF: 0.632

Asia WGS AF: 0.646 AC: 2249 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1390154; hg19: chr17-47071483;