rs10508272

Variant names:

• chr10-4014679-G-A
• rs10508272

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 0.0539 in 152,178 control chromosomes in the GnomAD database, including 278 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 0.054 (278 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.242

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.148 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: 0.0540 AC: 8208 AN: 152060 Hom.: 279 Cov.: 33

Gnomad AFR AF: 0.0379

Gnomad AMI AF: 0.0285

Gnomad AMR AF: 0.0477

Gnomad ASJ AF: 0.0697

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.0671

Gnomad FIN AF: 0.0227

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.0603

Gnomad OTH AF: 0.0598

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

GnomAD4 genome AF: 0.0539 AC: 8210 AN: 152178 Hom.: 278 Cov.: 33 AF XY: 0.0531 AC XY: 3952 AN XY: 74376

Gnomad4 AFR AF: 0.0380

Gnomad4 AMR AF: 0.0476

Gnomad4 ASJ AF: 0.0697

Gnomad4 EAS AF: 0.157

Gnomad4 SAS AF: 0.0678

Gnomad4 FIN AF: 0.0227

Gnomad4 NFE AF: 0.0603

Gnomad4 OTH AF: 0.0587

Alfa AF: 0.0586 Hom.: 183

Bravo AF: 0.0562

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.020
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10508272; hg19: chr10-4056871;