17-52367071-T-C

Variant names:

• chr17-52367071-T-C
• rs7212568

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 0.658 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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.911 AC: 37830 AN: 41540

American (AMR) AF: 0.711 AC: 10857 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.634 AC: 2200 AN: 3472

East Asian (EAS) AF: 0.494 AC: 2545 AN: 5152

South Asian (SAS) AF: 0.716 AC: 3449 AN: 4818

European-Finnish (FIN) AF: 0.546 AC: 5760 AN: 10546

Middle Eastern (MID) AF: 0.622 AC: 183 AN: 294

European-Non Finnish (NFE) AF: 0.521 AC: 35399 AN: 67938

Other (OTH) AF: 0.629 AC: 1330 AN: 2116

Alfa AF: 0.603 Hom.: 3837

Bravo AF: 0.677

Asia WGS AF: 0.667 AC: 2322 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.1
DANN	Benign	0.46
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs7212568; hg19: chr17-50444431;