rs9810857

Variant names:

• chr3-143264057-A-G
• rs9810857

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 0.404 in 152,102 control chromosomes in the GnomAD database, including 14,407 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 (14407 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.233
• Publications: 20 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.532 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: 0.404 AC: 61451 AN: 151984 Hom.: 14403 Cov.: 32

Gnomad AFR AF: 0.189

Gnomad AMI AF: 0.413

Gnomad AMR AF: 0.377

Gnomad ASJ AF: 0.440

Gnomad EAS AF: 0.112

Gnomad SAS AF: 0.398

Gnomad FIN AF: 0.566

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.537

Gnomad OTH AF: 0.427

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

GnomAD4 genome AF: 0.404 AC: 61455 AN: 152102 Hom.: 14407 Cov.: 32 AF XY: 0.400 AC XY: 29735 AN XY: 74370

African (AFR) AF: 0.189 AC: 7828 AN: 41504

American (AMR) AF: 0.376 AC: 5746 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.440 AC: 1528 AN: 3472

East Asian (EAS) AF: 0.112 AC: 578 AN: 5178

South Asian (SAS) AF: 0.399 AC: 1921 AN: 4814

European-Finnish (FIN) AF: 0.566 AC: 5979 AN: 10570

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.537 AC: 36483 AN: 67968

Other (OTH) AF: 0.424 AC: 895 AN: 2110

Alfa AF: 0.482 Hom.: 65519

Bravo AF: 0.375

Asia WGS AF: 0.234 AC: 815 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.0
DANN	Benign	0.38
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs9810857; hg19: chr3-142982899;