rs10065221

Variant names:

• chr5-132672516-A-G
• rs10065221

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 0.038 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.0826 AC: 3151 AN: 38158

American (AMR) AF: 0.0243 AC: 357 AN: 14688

Ashkenazi Jewish (ASJ) AF: 0.00118 AC: 4 AN: 3392

East Asian (EAS) AF: 0.200 AC: 1010 AN: 5046

South Asian (SAS) AF: 0.0353 AC: 159 AN: 4498

European-Finnish (FIN) AF: 0.0127 AC: 131 AN: 10288

Middle Eastern (MID) AF: 0.00746 AC: 2 AN: 268

European-Non Finnish (NFE) AF: 0.00994 AC: 661 AN: 66512

Other (OTH) AF: 0.0310 AC: 62 AN: 2002

Alfa AF: 0.0235 Hom.: 15

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.39
DANN	Benign	0.074
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs10065221; hg19: chr5-132008208;