rs4789070

Variant names:

• chr17-74498537-T-C
• rs4789070

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 0.441 in 152,010 control chromosomes in the GnomAD database, including 18,449 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 0.44 (18449 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.508

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.61 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: 0.441 AC: 67044 AN: 151892 Hom.: 18462 Cov.: 32

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.688

Gnomad AMR AF: 0.441

Gnomad ASJ AF: 0.634

Gnomad EAS AF: 0.246

Gnomad SAS AF: 0.451

Gnomad FIN AF: 0.577

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.615

Gnomad OTH AF: 0.493

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

GnomAD4 genome AF: 0.441 AC: 67012 AN: 152010 Hom.: 18449 Cov.: 32 AF XY: 0.437 AC XY: 32492 AN XY: 74294

Gnomad4 AFR AF: 0.119

Gnomad4 AMR AF: 0.441

Gnomad4 ASJ AF: 0.634

Gnomad4 EAS AF: 0.246

Gnomad4 SAS AF: 0.449

Gnomad4 FIN AF: 0.577

Gnomad4 NFE AF: 0.615

Gnomad4 OTH AF: 0.487

Alfa AF: 0.552 Hom.: 5138

Bravo AF: 0.417

Asia WGS AF: 0.299 AC: 1037 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.7
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4789070; hg19: chr17-72494676;