rs10488921

Variant names:

• chr4-57326034-C-T
• rs10488921

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.336 in 151,614 control chromosomes in the GnomAD database, including 8,889 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 0.34 (8889 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.344

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.429 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: 0.336 AC: 50948 AN: 151496 Hom.: 8889 Cov.: 31

Gnomad AFR AF: 0.250

Gnomad AMI AF: 0.321

Gnomad AMR AF: 0.351

Gnomad ASJ AF: 0.403

Gnomad EAS AF: 0.325

Gnomad SAS AF: 0.446

Gnomad FIN AF: 0.430

Gnomad MID AF: 0.365

Gnomad NFE AF: 0.361

Gnomad OTH AF: 0.338

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

GnomAD4 genome AF: 0.336 AC: 50961 AN: 151614 Hom.: 8889 Cov.: 31 AF XY: 0.341 AC XY: 25252 AN XY: 74048

Gnomad4 AFR AF: 0.249

Gnomad4 AMR AF: 0.350

Gnomad4 ASJ AF: 0.403

Gnomad4 EAS AF: 0.326

Gnomad4 SAS AF: 0.445

Gnomad4 FIN AF: 0.430

Gnomad4 NFE AF: 0.361

Gnomad4 OTH AF: 0.335

Alfa AF: 0.343 Hom.: 1435

Bravo AF: 0.320

Asia WGS AF: 0.361 AC: 1254 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	7.4
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10488921; hg19: chr4-58192200;