17-21256773-C-T

Variant names:

• chr17-21256773-C-T
• rs7217403

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 0.711 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
• Publications: 10 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.859 AC: 35665 AN: 41522

American (AMR) AF: 0.581 AC: 8870 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.644 AC: 2234 AN: 3470

East Asian (EAS) AF: 0.557 AC: 2876 AN: 5166

South Asian (SAS) AF: 0.692 AC: 3338 AN: 4822

European-Finnish (FIN) AF: 0.697 AC: 7362 AN: 10568

Middle Eastern (MID) AF: 0.690 AC: 203 AN: 294

European-Non Finnish (NFE) AF: 0.668 AC: 45380 AN: 67970

Other (OTH) AF: 0.688 AC: 1454 AN: 2112

Alfa AF: 0.680 Hom.: 22825

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
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs7217403; hg19: chr17-21160085;