rs4879670

Positions:

• chr9-33205410-T-C
• chr9-33205410-T-G

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 0.395 in 151,862 control chromosomes in the GnomAD database, including 12,239 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 0.40 (12239 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.385

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 (EAS) allele frequency at 95% confidence interval = 0.594 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: 0.395 AC: 60001 AN: 151744 Hom.: 12239 Cov.: 31

Gnomad AFR AF: 0.291

Gnomad AMI AF: 0.337

Gnomad AMR AF: 0.409

Gnomad ASJ AF: 0.445

Gnomad EAS AF: 0.612

Gnomad SAS AF: 0.423

Gnomad FIN AF: 0.426

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.431

Gnomad OTH AF: 0.401

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

GnomAD4 genome AF: 0.395 AC: 60006 AN: 151862 Hom.: 12239 Cov.: 31 AF XY: 0.396 AC XY: 29415 AN XY: 74206

Gnomad4 AFR AF: 0.291

Gnomad4 AMR AF: 0.408

Gnomad4 ASJ AF: 0.445

Gnomad4 EAS AF: 0.612

Gnomad4 SAS AF: 0.423

Gnomad4 FIN AF: 0.426

Gnomad4 NFE AF: 0.431

Gnomad4 OTH AF: 0.402

Alfa AF: 0.423 Hom.: 13645

Bravo AF: 0.395

Asia WGS AF: 0.485 AC: 1690 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	1.0
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4879670; hg19: chr9-33205408;