rs9877457

Variant names:

• chr3-135564539-A-G
• rs9877457

Your query was ambiguous. Multiple possible variants found:

• chr3-135564539-A-G
• chr3-135564539-A-T

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 0.489 in 152,078 control chromosomes in the GnomAD database, including 18,397 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 0.49 (18397 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.690
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.523 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: 0.489 AC: 74322 AN: 151960 Hom.: 18381 Cov.: 32

Gnomad AFR AF: 0.433

Gnomad AMI AF: 0.446

Gnomad AMR AF: 0.533

Gnomad ASJ AF: 0.535

Gnomad EAS AF: 0.460

Gnomad SAS AF: 0.377

Gnomad FIN AF: 0.520

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.516

Gnomad OTH AF: 0.509

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

GnomAD4 genome AF: 0.489 AC: 74369 AN: 152078 Hom.: 18397 Cov.: 32 AF XY: 0.485 AC XY: 36022 AN XY: 74332

African (AFR) AF: 0.433 AC: 17960 AN: 41474

American (AMR) AF: 0.533 AC: 8147 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.535 AC: 1856 AN: 3470

East Asian (EAS) AF: 0.460 AC: 2379 AN: 5176

South Asian (SAS) AF: 0.377 AC: 1820 AN: 4822

European-Finnish (FIN) AF: 0.520 AC: 5486 AN: 10548

Middle Eastern (MID) AF: 0.582 AC: 171 AN: 294

European-Non Finnish (NFE) AF: 0.516 AC: 35076 AN: 67984

Other (OTH) AF: 0.506 AC: 1068 AN: 2112

Alfa AF: 0.493 Hom.: 2255

Bravo AF: 0.494

Asia WGS AF: 0.392 AC: 1364 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	7.4
DANN	Benign	0.73
PhyloP100		-0.69

Splicing

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

Other links and lift over

dbSNP: rs9877457; hg19: chr3-135283381;