rs4969198

Variant names:

• chr17-78588303-A-G
• rs4969198

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 0.665 in 152,150 control chromosomes in the GnomAD database, including 35,521 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 (35521 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.10
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.882 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: 0.665 AC: 101044 AN: 152032 Hom.: 35462 Cov.: 32

Gnomad AFR AF: 0.890

Gnomad AMI AF: 0.737

Gnomad AMR AF: 0.721

Gnomad ASJ AF: 0.520

Gnomad EAS AF: 0.363

Gnomad SAS AF: 0.569

Gnomad FIN AF: 0.507

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.576

Gnomad OTH AF: 0.651

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

GnomAD4 genome AF: 0.665 AC: 101167 AN: 152150 Hom.: 35521 Cov.: 32 AF XY: 0.660 AC XY: 49078 AN XY: 74392

African (AFR) AF: 0.890 AC: 36947 AN: 41530

American (AMR) AF: 0.722 AC: 11034 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.520 AC: 1804 AN: 3470

East Asian (EAS) AF: 0.363 AC: 1877 AN: 5168

South Asian (SAS) AF: 0.568 AC: 2741 AN: 4826

European-Finnish (FIN) AF: 0.507 AC: 5373 AN: 10590

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

European-Non Finnish (NFE) AF: 0.576 AC: 39157 AN: 67964

Other (OTH) AF: 0.653 AC: 1380 AN: 2112

Alfa AF: 0.648 Hom.: 4269

Bravo AF: 0.690

Asia WGS AF: 0.555 AC: 1926 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.28
DANN	Benign	0.40
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs4969198; hg19: chr17-76584385;