rs10065221

Variant names:

• chr5-132672516-A-G
• rs10065221

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 0.038 in 145,748 control chromosomes in the GnomAD database, including 306 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 0.038 (306 hom., cov: 26)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.457

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.19 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: 0.0380 AC: 5537 AN: 145636 Hom.: 305 Cov.: 26

Gnomad AFR AF: 0.0826

Gnomad AMI AF: 0.00112

Gnomad AMR AF: 0.0245

Gnomad ASJ AF: 0.00118

Gnomad EAS AF: 0.200

Gnomad SAS AF: 0.0357

Gnomad FIN AF: 0.0127

Gnomad MID AF: 0.00699

Gnomad NFE AF: 0.00995

Gnomad OTH AF: 0.0313

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

GnomAD4 genome AF: 0.0380 AC: 5538 AN: 145748 Hom.: 306 Cov.: 26 AF XY: 0.0388 AC XY: 2758 AN XY: 71046

Gnomad4 AFR AF: 0.0826

Gnomad4 AMR AF: 0.0243

Gnomad4 ASJ AF: 0.00118

Gnomad4 EAS AF: 0.200

Gnomad4 SAS AF: 0.0353

Gnomad4 FIN AF: 0.0127

Gnomad4 NFE AF: 0.00994

Gnomad4 OTH AF: 0.0310

Alfa AF: 0.0230 Hom.: 15

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.39
DANN	Benign	0.074

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10065221; hg19: chr5-132008208;