20-63638589-C-T

Variant names:

• chr20-63638589-C-T
• rs879471

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 0.43 in 152,122 control chromosomes in the GnomAD database, including 15,878 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 0.43 (15878 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.41
• Publications: 17 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 (NFE) allele frequency at 95% confidence interval = 0.557 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: 0.430 AC: 65416 AN: 152002 Hom.: 15880 Cov.: 33

Gnomad AFR AF: 0.241

Gnomad AMI AF: 0.497

Gnomad AMR AF: 0.442

Gnomad ASJ AF: 0.551

Gnomad EAS AF: 0.113

Gnomad SAS AF: 0.289

Gnomad FIN AF: 0.480

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.561

Gnomad OTH AF: 0.462

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

GnomAD4 genome AF: 0.430 AC: 65418 AN: 152122 Hom.: 15878 Cov.: 33 AF XY: 0.424 AC XY: 31512 AN XY: 74358

African (AFR) AF: 0.240 AC: 9980 AN: 41532

American (AMR) AF: 0.442 AC: 6751 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.551 AC: 1912 AN: 3472

East Asian (EAS) AF: 0.113 AC: 583 AN: 5178

South Asian (SAS) AF: 0.289 AC: 1394 AN: 4822

European-Finnish (FIN) AF: 0.480 AC: 5073 AN: 10572

Middle Eastern (MID) AF: 0.524 AC: 153 AN: 292

European-Non Finnish (NFE) AF: 0.561 AC: 38157 AN: 67958

Other (OTH) AF: 0.458 AC: 963 AN: 2104

Alfa AF: 0.531 Hom.: 42616

Bravo AF: 0.421

Asia WGS AF: 0.191 AC: 666 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.35
DANN	Benign	0.30
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs879471; hg19: chr20-62269942;