rs12451970

Variant names:

• chr17-65499636-G-T
• rs12451970

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 0.108 in 144,366 control chromosomes in the GnomAD database, including 1,107 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 0.11 (1107 hom., cov: 24)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.174
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.18 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.108 AC: 15602 AN: 144280 Hom.: 1109 Cov.: 24

Gnomad AFR AF: 0.0256

Gnomad AMI AF: 0.0889

Gnomad AMR AF: 0.0845

Gnomad ASJ AF: 0.227

Gnomad EAS AF: 0.0690

Gnomad SAS AF: 0.190

Gnomad FIN AF: 0.149

Gnomad MID AF: 0.205

Gnomad NFE AF: 0.146

Gnomad OTH AF: 0.131

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

GnomAD4 genome AF: 0.108 AC: 15585 AN: 144366 Hom.: 1107 Cov.: 24 AF XY: 0.108 AC XY: 7548 AN XY: 69710

African (AFR) AF: 0.0255 AC: 994 AN: 38970

American (AMR) AF: 0.0844 AC: 1177 AN: 13952

Ashkenazi Jewish (ASJ) AF: 0.227 AC: 777 AN: 3418

East Asian (EAS) AF: 0.0690 AC: 326 AN: 4726

South Asian (SAS) AF: 0.191 AC: 837 AN: 4386

European-Finnish (FIN) AF: 0.149 AC: 1366 AN: 9142

Middle Eastern (MID) AF: 0.184 AC: 52 AN: 282

European-Non Finnish (NFE) AF: 0.146 AC: 9719 AN: 66596

Other (OTH) AF: 0.129 AC: 257 AN: 1994

Alfa AF: 0.139 Hom.: 1797

Bravo AF: 0.0999

Asia WGS AF: 0.101 AC: 354 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.0
DANN	Benign	0.68
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs12451970; hg19: chr17-63495754;