rs1455528

chr17-41554594-C-G

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 0.951 in 151,950 control chromosomes in the GnomAD database, including 68,990 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 0.95 (68977 hom., cov: 27)
  • Exomes 𝑓: 0.96 (13 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.269

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.985 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.951 AC: 144375 AN: 151804 Hom.: 68949 Cov.: 27

Gnomad AFR AF: 0.846

Gnomad AMI AF: 0.998

Gnomad AMR AF: 0.978

Gnomad ASJ AF: 0.997

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.987

Gnomad FIN AF: 0.997

Gnomad MID AF: 0.987

Gnomad NFE AF: 0.992

Gnomad OTH AF: 0.959

GnomAD4 exome AF: 0.964 AC: 27 AN: 28 Hom.: 13 AF XY: 0.955 AC XY: 21 AN XY: 22

Gnomad4 NFE exome AF: 0.964

GnomAD4 genome AF: 0.951 AC: 144455 AN: 151922 Hom.: 68977 Cov.: 27 AF XY: 0.952 AC XY: 70682 AN XY: 74258

Gnomad4 AFR AF: 0.846

Gnomad4 AMR AF: 0.978

Gnomad4 ASJ AF: 0.997

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.987

Gnomad4 FIN AF: 0.997

Gnomad4 NFE AF: 0.992

Gnomad4 OTH AF: 0.957

Alfa AF: 0.969 Hom.: 8886

Bravo AF: 0.944

Asia WGS AF: 0.971 AC: 3377 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	1.3
Dann	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1455528; hg19: chr17-39710846;