17-74272069-A-G

Variant names:

• chr17-74272069-A-G
• rs7219585

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 0.876 in 151,544 control chromosomes in the GnomAD database, including 58,184 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 0.88 (58184 hom., cov: 26)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.122
• Publications: 12 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 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: 0.876 AC: 132587 AN: 151426 Hom.: 58147 Cov.: 26

Gnomad AFR AF: 0.878

Gnomad AMI AF: 0.902

Gnomad AMR AF: 0.848

Gnomad ASJ AF: 0.850

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.931

Gnomad FIN AF: 0.890

Gnomad MID AF: 0.924

Gnomad NFE AF: 0.865

Gnomad OTH AF: 0.874

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

GnomAD4 genome AF: 0.876 AC: 132679 AN: 151544 Hom.: 58184 Cov.: 26 AF XY: 0.878 AC XY: 64915 AN XY: 73974

African (AFR) AF: 0.878 AC: 36223 AN: 41248

American (AMR) AF: 0.848 AC: 12864 AN: 15174

Ashkenazi Jewish (ASJ) AF: 0.850 AC: 2949 AN: 3468

East Asian (EAS) AF: 0.998 AC: 5092 AN: 5102

South Asian (SAS) AF: 0.931 AC: 4465 AN: 4798

European-Finnish (FIN) AF: 0.890 AC: 9383 AN: 10538

Middle Eastern (MID) AF: 0.918 AC: 270 AN: 294

European-Non Finnish (NFE) AF: 0.865 AC: 58779 AN: 67918

Other (OTH) AF: 0.875 AC: 1835 AN: 2096

Alfa AF: 0.871 Hom.: 125623

Bravo AF: 0.872

Asia WGS AF: 0.963 AC: 3348 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	6.0
DANN	Benign	0.66
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs7219585; hg19: chr17-72268208;