rs10488918

Positions:

• chr4-57344774-T-C

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 0.0511 in 152,240 control chromosomes in the GnomAD database, including 322 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 0.051 (322 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.283

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.212 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0512 AC: 7795 AN: 152122 Hom.: 325 Cov.: 33

Gnomad AFR AF: 0.0119

Gnomad AMI AF: 0.0154

Gnomad AMR AF: 0.0416

Gnomad ASJ AF: 0.0706

Gnomad EAS AF: 0.224

Gnomad SAS AF: 0.0740

Gnomad FIN AF: 0.0367

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0646

Gnomad OTH AF: 0.0464

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

GnomAD4 genome AF: 0.0511 AC: 7787 AN: 152240 Hom.: 322 Cov.: 33 AF XY: 0.0512 AC XY: 3808 AN XY: 74436

Gnomad4 AFR AF: 0.0119

Gnomad4 AMR AF: 0.0416

Gnomad4 ASJ AF: 0.0706

Gnomad4 EAS AF: 0.223

Gnomad4 SAS AF: 0.0740

Gnomad4 FIN AF: 0.0367

Gnomad4 NFE AF: 0.0646

Gnomad4 OTH AF: 0.0464

Alfa AF: 0.0578 Hom.: 139

Bravo AF: 0.0494

Asia WGS AF: 0.126 AC: 438 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	6.6
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: rs10488918; hg19: chr4-58210940;