rs10516248

chr4-12184821-A-Cchr4-12184821-A-Gchr4-12184821-A-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 0.712 in 151,936 control chromosomes in the GnomAD database, including 38,646 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 0.71 (38646 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.72 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: 0.712 AC: 108097 AN: 151818 Hom.: 38588 Cov.: 31

Gnomad AFR AF: 0.695

Gnomad AMI AF: 0.532

Gnomad AMR AF: 0.702

Gnomad ASJ AF: 0.723

Gnomad EAS AF: 0.740

Gnomad SAS AF: 0.635

Gnomad FIN AF: 0.779

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.720

Gnomad OTH AF: 0.712

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

GnomAD4 genome AF: 0.712 AC: 108211 AN: 151936 Hom.: 38646 Cov.: 31 AF XY: 0.712 AC XY: 52897 AN XY: 74250

Gnomad4 AFR AF: 0.695

Gnomad4 AMR AF: 0.703

Gnomad4 ASJ AF: 0.723

Gnomad4 EAS AF: 0.740

Gnomad4 SAS AF: 0.636

Gnomad4 FIN AF: 0.779

Gnomad4 NFE AF: 0.720

Gnomad4 OTH AF: 0.710

Alfa AF: 0.713 Hom.: 62452

Bravo AF: 0.704

Asia WGS AF: 0.667 AC: 2324 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.8
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: rs10516248; hg19: chr4-12186445;