rs2804402

Variant names:

• chr10-99781826-A-G
• rs2804402

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 0.389 in 152,176 control chromosomes in the GnomAD database, including 11,838 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 0.39 (11838 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.834
• Publications: 24 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.423 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: 0.389 AC: 59126 AN: 152058 Hom.: 11835 Cov.: 33

Gnomad AFR AF: 0.330

Gnomad AMI AF: 0.529

Gnomad AMR AF: 0.418

Gnomad ASJ AF: 0.472

Gnomad EAS AF: 0.231

Gnomad SAS AF: 0.375

Gnomad FIN AF: 0.364

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.427

Gnomad OTH AF: 0.425

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

GnomAD4 genome AF: 0.389 AC: 59164 AN: 152176 Hom.: 11838 Cov.: 33 AF XY: 0.386 AC XY: 28702 AN XY: 74394

African (AFR) AF: 0.330 AC: 13691 AN: 41492

American (AMR) AF: 0.418 AC: 6388 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.472 AC: 1637 AN: 3470

East Asian (EAS) AF: 0.230 AC: 1194 AN: 5186

South Asian (SAS) AF: 0.375 AC: 1812 AN: 4828

European-Finnish (FIN) AF: 0.364 AC: 3853 AN: 10596

Middle Eastern (MID) AF: 0.497 AC: 146 AN: 294

European-Non Finnish (NFE) AF: 0.427 AC: 29059 AN: 68002

Other (OTH) AF: 0.428 AC: 902 AN: 2108

Alfa AF: 0.537 Hom.: 8221

Bravo AF: 0.389

Asia WGS AF: 0.335 AC: 1165 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.9
DANN	Benign	0.50
PhyloP100		-0.83

Splicing

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

Other links and lift over

dbSNP: rs2804402; hg19: chr10-101541583;