rs4969198

Variant names:

• chr17-78588303-A-G
• rs4969198

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 0.665 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.665 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

Gnomad4 AFR AF: 0.890

Gnomad4 AMR AF: 0.722

Gnomad4 ASJ AF: 0.520

Gnomad4 EAS AF: 0.363

Gnomad4 SAS AF: 0.568

Gnomad4 FIN AF: 0.507

Gnomad4 NFE AF: 0.576

Gnomad4 OTH AF: 0.653

Alfa AF: 0.638 Hom.: 3961

Bravo AF: 0.690

Asia WGS AF: 0.555 AC: 1926 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4969198; hg19: chr17-76584385;