17-16973769-A-G

Variant names:

• chr17-16973769-A-G
• rs7504096

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 0.86 in 152,314 control chromosomes in the GnomAD database, including 56,783 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 0.86 (56783 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.43
• Publications: 6 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 = 0.976 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: 0.860 AC: 130923 AN: 152194 Hom.: 56725 Cov.: 34

Gnomad AFR AF: 0.962

Gnomad AMI AF: 0.901

Gnomad AMR AF: 0.851

Gnomad ASJ AF: 0.797

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.875

Gnomad FIN AF: 0.792

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.803

Gnomad OTH AF: 0.839

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

GnomAD4 genome AF: 0.860 AC: 131041 AN: 152314 Hom.: 56783 Cov.: 34 AF XY: 0.862 AC XY: 64173 AN XY: 74476

African (AFR) AF: 0.962 AC: 40006 AN: 41574

American (AMR) AF: 0.851 AC: 13027 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.797 AC: 2766 AN: 3472

East Asian (EAS) AF: 0.999 AC: 5181 AN: 5188

South Asian (SAS) AF: 0.875 AC: 4220 AN: 4822

European-Finnish (FIN) AF: 0.792 AC: 8395 AN: 10606

Middle Eastern (MID) AF: 0.803 AC: 236 AN: 294

European-Non Finnish (NFE) AF: 0.803 AC: 54610 AN: 68024

Other (OTH) AF: 0.840 AC: 1778 AN: 2116

Alfa AF: 0.825 Hom.: 65461

Bravo AF: 0.869

Asia WGS AF: 0.946 AC: 3290 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.13
DANN	Benign	0.18
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs7504096; hg19: chr17-16877083;