17-52367071-T-C

Variant names:

• chr17-52367071-T-C
• rs7212568

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 0.658 in 152,056 control chromosomes in the GnomAD database, including 35,065 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 0.66 (35065 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.158

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.903 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: 0.658 AC: 99974 AN: 151938 Hom.: 35007 Cov.: 31

Gnomad AFR AF: 0.910

Gnomad AMI AF: 0.588

Gnomad AMR AF: 0.711

Gnomad ASJ AF: 0.634

Gnomad EAS AF: 0.494

Gnomad SAS AF: 0.716

Gnomad FIN AF: 0.546

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.521

Gnomad OTH AF: 0.629

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

GnomAD4 genome AF: 0.658 AC: 100089 AN: 152056 Hom.: 35065 Cov.: 31 AF XY: 0.660 AC XY: 49052 AN XY: 74312

Gnomad4 AFR AF: 0.911

Gnomad4 AMR AF: 0.711

Gnomad4 ASJ AF: 0.634

Gnomad4 EAS AF: 0.494

Gnomad4 SAS AF: 0.716

Gnomad4 FIN AF: 0.546

Gnomad4 NFE AF: 0.521

Gnomad4 OTH AF: 0.629

Alfa AF: 0.591 Hom.: 3510

Bravo AF: 0.677

Asia WGS AF: 0.667 AC: 2322 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.1
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7212568; hg19: chr17-50444431;