rs4980248

chr10-123067649-C-Achr10-123067649-C-T

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 0.375 in 151,966 control chromosomes in the GnomAD database, including 10,978 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 0.37 (10978 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0620

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.417 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.375 AC: 56900 AN: 151848 Hom.: 10968 Cov.: 31

Gnomad AFR AF: 0.375

Gnomad AMI AF: 0.524

Gnomad AMR AF: 0.369

Gnomad ASJ AF: 0.336

Gnomad EAS AF: 0.103

Gnomad SAS AF: 0.431

Gnomad FIN AF: 0.411

Gnomad MID AF: 0.360

Gnomad NFE AF: 0.387

Gnomad OTH AF: 0.381

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

GnomAD4 genome AF: 0.375 AC: 56947 AN: 151966 Hom.: 10978 Cov.: 31 AF XY: 0.375 AC XY: 27840 AN XY: 74266

Gnomad4 AFR AF: 0.375

Gnomad4 AMR AF: 0.369

Gnomad4 ASJ AF: 0.336

Gnomad4 EAS AF: 0.103

Gnomad4 SAS AF: 0.432

Gnomad4 FIN AF: 0.411

Gnomad4 NFE AF: 0.387

Gnomad4 OTH AF: 0.380

Alfa AF: 0.384 Hom.: 14691

Bravo AF: 0.370

Asia WGS AF: 0.311 AC: 1084 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.80
Dann	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4980248; hg19: chr10-124827165;