rs7217373

Variant names:

• chr17-21256718-C-G
• rs7217373

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 152,038 control chromosomes in the GnomAD database, including 39,165 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 (39165 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.737

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.852 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: 107965 AN: 151918 Hom.: 39125 Cov.: 31

Gnomad AFR AF: 0.859

Gnomad AMI AF: 0.830

Gnomad AMR AF: 0.580

Gnomad ASJ AF: 0.644

Gnomad EAS AF: 0.556

Gnomad SAS AF: 0.691

Gnomad FIN AF: 0.697

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.667

Gnomad OTH AF: 0.686

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

GnomAD4 genome AF: 0.711 AC: 108063 AN: 152038 Hom.: 39165 Cov.: 31 AF XY: 0.709 AC XY: 52658 AN XY: 74290

Gnomad4 AFR AF: 0.859

Gnomad4 AMR AF: 0.580

Gnomad4 ASJ AF: 0.644

Gnomad4 EAS AF: 0.556

Gnomad4 SAS AF: 0.692

Gnomad4 FIN AF: 0.697

Gnomad4 NFE AF: 0.667

Gnomad4 OTH AF: 0.687

Alfa AF: 0.696 Hom.: 4613

Bravo AF: 0.704

Asia WGS AF: 0.664 AC: 2312 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.64
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7217373; hg19: chr17-21160030;