rs1472081

Variant names:

• chr17-29068872-C-T
• rs1472081

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 0.368 in 152,118 control chromosomes in the GnomAD database, including 11,047 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 (11047 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.896

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.52).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.821 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: 0.368 AC: 55977 AN: 152000 Hom.: 11040 Cov.: 33

Gnomad AFR AF: 0.405

Gnomad AMI AF: 0.383

Gnomad AMR AF: 0.346

Gnomad ASJ AF: 0.370

Gnomad EAS AF: 0.842

Gnomad SAS AF: 0.388

Gnomad FIN AF: 0.323

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.321

Gnomad OTH AF: 0.364

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

GnomAD4 genome AF: 0.368 AC: 56028 AN: 152118 Hom.: 11047 Cov.: 33 AF XY: 0.369 AC XY: 27464 AN XY: 74358

Gnomad4 AFR AF: 0.405

Gnomad4 AMR AF: 0.346

Gnomad4 ASJ AF: 0.370

Gnomad4 EAS AF: 0.842

Gnomad4 SAS AF: 0.388

Gnomad4 FIN AF: 0.323

Gnomad4 NFE AF: 0.321

Gnomad4 OTH AF: 0.370

Alfa AF: 0.329 Hom.: 10454

Bravo AF: 0.374

Asia WGS AF: 0.574 AC: 1993 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
CADD	Benign	16
DANN	Benign	0.95

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1472081; hg19: chr17-27395890;