rs10003827

Variant names:

• chr4-122809698-T-C
• rs10003827

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 0.228 in 152,182 control chromosomes in the GnomAD database, including 5,568 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 0.23 (5568 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.24
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.438 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: 0.228 AC: 34694 AN: 152062 Hom.: 5550 Cov.: 33

Gnomad AFR AF: 0.443

Gnomad AMI AF: 0.208

Gnomad AMR AF: 0.234

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.118

Gnomad SAS AF: 0.285

Gnomad FIN AF: 0.0559

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.235

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

GnomAD4 genome AF: 0.228 AC: 34762 AN: 152182 Hom.: 5568 Cov.: 33 AF XY: 0.225 AC XY: 16749 AN XY: 74420

African (AFR) AF: 0.443 AC: 18369 AN: 41476

American (AMR) AF: 0.235 AC: 3590 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.255 AC: 885 AN: 3470

East Asian (EAS) AF: 0.118 AC: 611 AN: 5196

South Asian (SAS) AF: 0.285 AC: 1372 AN: 4818

European-Finnish (FIN) AF: 0.0559 AC: 594 AN: 10622

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.126 AC: 8574 AN: 68002

Other (OTH) AF: 0.233 AC: 492 AN: 2110

Alfa AF: 0.171 Hom.: 3110

Bravo AF: 0.254

Asia WGS AF: 0.270 AC: 935 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.23
DANN	Benign	0.77
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs10003827; hg19: chr4-123730853;