rs20451

Variant names:

• chr7-145499433-T-C
• rs20451

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 0.121 in 152,228 control chromosomes in the GnomAD database, including 3,063 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 0.12 (3063 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.374 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: 0.120 AC: 18312 AN: 152110 Hom.: 3054 Cov.: 33

Gnomad AFR AF: 0.378

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.0431

Gnomad ASJ AF: 0.0838

Gnomad EAS AF: 0.0553

Gnomad SAS AF: 0.0313

Gnomad FIN AF: 0.00386

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0148

Gnomad OTH AF: 0.0964

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

GnomAD4 genome AF: 0.121 AC: 18360 AN: 152228 Hom.: 3063 Cov.: 33 AF XY: 0.117 AC XY: 8681 AN XY: 74424

African (AFR) AF: 0.379 AC: 15708 AN: 41488

American (AMR) AF: 0.0429 AC: 656 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0838 AC: 291 AN: 3472

East Asian (EAS) AF: 0.0552 AC: 286 AN: 5180

South Asian (SAS) AF: 0.0303 AC: 146 AN: 4826

European-Finnish (FIN) AF: 0.00386 AC: 41 AN: 10616

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0148 AC: 1005 AN: 68030

Other (OTH) AF: 0.0954 AC: 201 AN: 2108

Alfa AF: 0.0906 Hom.: 298

Bravo AF: 0.136

Asia WGS AF: 0.0610 AC: 213 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.85
DANN	Benign	0.75
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs20451; hg19: chr7-145196526;