rs3849221

Variant names:

• chr9-135136831-A-C
• rs3849221

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 0.59 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
• Publications: 4 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 (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

African (AFR) AF: 0.344 AC: 14265 AN: 41462

American (AMR) AF: 0.612 AC: 9350 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.684 AC: 2374 AN: 3470

East Asian (EAS) AF: 0.533 AC: 2743 AN: 5144

South Asian (SAS) AF: 0.661 AC: 3179 AN: 4806

European-Finnish (FIN) AF: 0.712 AC: 7521 AN: 10568

Middle Eastern (MID) AF: 0.616 AC: 181 AN: 294

European-Non Finnish (NFE) AF: 0.710 AC: 48275 AN: 68006

Other (OTH) AF: 0.598 AC: 1264 AN: 2112

Alfa AF: 0.599 Hom.: 23956

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
PhyloP100		-0.038

Splicing

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

Other links and lift over

dbSNP: rs3849221; hg19: chr9-138028677;