rs10516248

Variant names:

• chr4-12184821-A-C
• rs10516248

Your query was ambiguous. Multiple possible variants found:

• chr4-12184821-A-C
• chr4-12184821-A-G
• chr4-12184821-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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;