17-21256773-C-T

Position:

• chr17-21256773-C-T

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 0.711 in 152,102 control chromosomes in the GnomAD database, including 39,205 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 0.71 (39205 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.346

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.851 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: 0.711 AC: 108039 AN: 151984 Hom.: 39165 Cov.: 32

Gnomad AFR AF: 0.859

Gnomad AMI AF: 0.828

Gnomad AMR AF: 0.582

Gnomad ASJ AF: 0.644

Gnomad EAS AF: 0.557

Gnomad SAS AF: 0.691

Gnomad FIN AF: 0.697

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.668

Gnomad OTH AF: 0.687

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

GnomAD4 genome AF: 0.711 AC: 108137 AN: 152102 Hom.: 39205 Cov.: 32 AF XY: 0.709 AC XY: 52692 AN XY: 74320

Gnomad4 AFR AF: 0.859

Gnomad4 AMR AF: 0.581

Gnomad4 ASJ AF: 0.644

Gnomad4 EAS AF: 0.557

Gnomad4 SAS AF: 0.692

Gnomad4 FIN AF: 0.697

Gnomad4 NFE AF: 0.668

Gnomad4 OTH AF: 0.688

Alfa AF: 0.679 Hom.: 20756

Bravo AF: 0.704

Asia WGS AF: 0.664 AC: 2313 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.76
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7217403; hg19: chr17-21160085;