rs4789070

chr17-74498537-T-C

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;