rs4980248

Variant names:

• chr10-123067649-C-A
• rs4980248

Your query was ambiguous. Multiple possible variants found:

• chr10-123067649-C-A
• chr10-123067649-C-T

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 0.375 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.375 AC: 15516 AN: 41396

American (AMR) AF: 0.369 AC: 5631 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.336 AC: 1165 AN: 3472

East Asian (EAS) AF: 0.103 AC: 533 AN: 5178

South Asian (SAS) AF: 0.432 AC: 2085 AN: 4822

European-Finnish (FIN) AF: 0.411 AC: 4339 AN: 10550

Middle Eastern (MID) AF: 0.366 AC: 107 AN: 292

European-Non Finnish (NFE) AF: 0.387 AC: 26294 AN: 67974

Other (OTH) AF: 0.380 AC: 800 AN: 2106

Alfa AF: 0.384 Hom.: 18732

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
PhyloP100		-0.062

Splicing

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

Other links and lift over

dbSNP: rs4980248; hg19: chr10-124827165;