rs4790069

Variant names:

• chr17-79053619-T-C
• rs4790069

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 0.376 in 151,374 control chromosomes in the GnomAD database, including 12,719 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 0.38 (12719 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.628
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.567 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: 0.376 AC: 56876 AN: 151256 Hom.: 12683 Cov.: 31

Gnomad AFR AF: 0.571

Gnomad AMI AF: 0.362

Gnomad AMR AF: 0.421

Gnomad ASJ AF: 0.323

Gnomad EAS AF: 0.583

Gnomad SAS AF: 0.424

Gnomad FIN AF: 0.211

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.261

Gnomad OTH AF: 0.335

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

GnomAD4 genome AF: 0.376 AC: 56974 AN: 151374 Hom.: 12719 Cov.: 31 AF XY: 0.376 AC XY: 27847 AN XY: 73974

African (AFR) AF: 0.571 AC: 23316 AN: 40834

American (AMR) AF: 0.422 AC: 6424 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.323 AC: 1122 AN: 3472

East Asian (EAS) AF: 0.584 AC: 3018 AN: 5168

South Asian (SAS) AF: 0.424 AC: 2043 AN: 4824

European-Finnish (FIN) AF: 0.211 AC: 2231 AN: 10578

Middle Eastern (MID) AF: 0.252 AC: 73 AN: 290

European-Non Finnish (NFE) AF: 0.261 AC: 17706 AN: 67964

Other (OTH) AF: 0.339 AC: 712 AN: 2098

Alfa AF: 0.288 Hom.: 7487

Bravo AF: 0.401

Asia WGS AF: 0.515 AC: 1790 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.6
DANN	Benign	0.74
PhyloP100		0.63

Splicing

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

Other links and lift over

dbSNP: rs4790069; hg19: chr17-77049701;