20-5631240-T-C

Variant names:

• chr20-5631240-T-C
• rs2102486

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 0.384 in 151,928 control chromosomes in the GnomAD database, including 12,274 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 0.38 (12274 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.785
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.494 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: 0.384 AC: 58334 AN: 151810 Hom.: 12264 Cov.: 31

Gnomad AFR AF: 0.194

Gnomad AMI AF: 0.615

Gnomad AMR AF: 0.502

Gnomad ASJ AF: 0.499

Gnomad EAS AF: 0.406

Gnomad SAS AF: 0.512

Gnomad FIN AF: 0.409

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.449

Gnomad OTH AF: 0.401

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

GnomAD4 genome AF: 0.384 AC: 58350 AN: 151928 Hom.: 12274 Cov.: 31 AF XY: 0.387 AC XY: 28731 AN XY: 74238

African (AFR) AF: 0.194 AC: 8029 AN: 41460

American (AMR) AF: 0.503 AC: 7662 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.499 AC: 1734 AN: 3472

East Asian (EAS) AF: 0.405 AC: 2095 AN: 5172

South Asian (SAS) AF: 0.511 AC: 2460 AN: 4812

European-Finnish (FIN) AF: 0.409 AC: 4322 AN: 10558

Middle Eastern (MID) AF: 0.524 AC: 154 AN: 294

European-Non Finnish (NFE) AF: 0.449 AC: 30501 AN: 67912

Other (OTH) AF: 0.396 AC: 835 AN: 2106

Alfa AF: 0.429 Hom.: 39799

Bravo AF: 0.381

Asia WGS AF: 0.433 AC: 1510 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.23
DANN	Benign	0.30
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs2102486; hg19: chr20-5611886;