chr20-32978321-T-C

Variant names:

• chr20-32978321-T-C
• rs751695

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 0.549 in 151,868 control chromosomes in the GnomAD database, including 23,770 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 0.55 (23770 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.938
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.634 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: 0.549 AC: 83352 AN: 151750 Hom.: 23743 Cov.: 31

Gnomad AFR AF: 0.640

Gnomad AMI AF: 0.531

Gnomad AMR AF: 0.544

Gnomad ASJ AF: 0.555

Gnomad EAS AF: 0.0757

Gnomad SAS AF: 0.369

Gnomad FIN AF: 0.585

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.538

Gnomad OTH AF: 0.567

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

GnomAD4 genome AF: 0.549 AC: 83426 AN: 151868 Hom.: 23770 Cov.: 31 AF XY: 0.547 AC XY: 40626 AN XY: 74206

African (AFR) AF: 0.641 AC: 26524 AN: 41402

American (AMR) AF: 0.543 AC: 8282 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.555 AC: 1926 AN: 3470

East Asian (EAS) AF: 0.0757 AC: 392 AN: 5178

South Asian (SAS) AF: 0.367 AC: 1764 AN: 4804

European-Finnish (FIN) AF: 0.585 AC: 6179 AN: 10554

Middle Eastern (MID) AF: 0.612 AC: 180 AN: 294

European-Non Finnish (NFE) AF: 0.538 AC: 36507 AN: 67916

Other (OTH) AF: 0.568 AC: 1192 AN: 2100

Alfa AF: 0.536 Hom.: 93308

Bravo AF: 0.547

Asia WGS AF: 0.297 AC: 1035 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.0
DANN	Benign	0.51
PhyloP100		-0.94

Splicing

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

Other links and lift over

dbSNP: rs751695; hg19: chr20-31566127;