rs4879670

Variant names:

• chr9-33205410-T-C
• rs4879670

Your query was ambiguous. Multiple possible variants found:

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

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 0.395 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
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.291 AC: 12031 AN: 41378

American (AMR) AF: 0.408 AC: 6237 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.445 AC: 1542 AN: 3466

East Asian (EAS) AF: 0.612 AC: 3159 AN: 5162

South Asian (SAS) AF: 0.423 AC: 2033 AN: 4806

European-Finnish (FIN) AF: 0.426 AC: 4484 AN: 10530

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.431 AC: 29262 AN: 67940

Other (OTH) AF: 0.402 AC: 848 AN: 2110

Alfa AF: 0.421 Hom.: 16314

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
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs4879670; hg19: chr9-33205408;