rs3849221

Variant names:

• chr9-135136831-A-C
• rs3849221

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 0.59 in 152,050 control chromosomes in the GnomAD database, including 28,458 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 0.59 (28458 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0380

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 = 0.705 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: 0.591 AC: 89729 AN: 151932 Hom.: 28456 Cov.: 32

Gnomad AFR AF: 0.344

Gnomad AMI AF: 0.650

Gnomad AMR AF: 0.612

Gnomad ASJ AF: 0.684

Gnomad EAS AF: 0.534

Gnomad SAS AF: 0.663

Gnomad FIN AF: 0.712

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.710

Gnomad OTH AF: 0.598

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

GnomAD4 genome AF: 0.590 AC: 89745 AN: 152050 Hom.: 28458 Cov.: 32 AF XY: 0.592 AC XY: 43993 AN XY: 74314

Gnomad4 AFR AF: 0.344

Gnomad4 AMR AF: 0.612

Gnomad4 ASJ AF: 0.684

Gnomad4 EAS AF: 0.533

Gnomad4 SAS AF: 0.661

Gnomad4 FIN AF: 0.712

Gnomad4 NFE AF: 0.710

Gnomad4 OTH AF: 0.598

Alfa AF: 0.645 Hom.: 11215

Bravo AF: 0.571

Asia WGS AF: 0.608 AC: 2113 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	2.4
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3849221; hg19: chr9-138028677;