20-5611257-T-G

Variant names:

• chr20-5611257-T-G
• rs238288

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 0.693 in 152,192 control chromosomes in the GnomAD database, including 37,444 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 0.69 (37444 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.487
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.55).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.834 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: 0.693 AC: 105375 AN: 152078 Hom.: 37407 Cov.: 34

Gnomad AFR AF: 0.842

Gnomad AMI AF: 0.659

Gnomad AMR AF: 0.657

Gnomad ASJ AF: 0.704

Gnomad EAS AF: 0.731

Gnomad SAS AF: 0.634

Gnomad FIN AF: 0.507

Gnomad MID AF: 0.706

Gnomad NFE AF: 0.641

Gnomad OTH AF: 0.685

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

GnomAD4 genome AF: 0.693 AC: 105460 AN: 152192 Hom.: 37444 Cov.: 34 AF XY: 0.687 AC XY: 51147 AN XY: 74402

African (AFR) AF: 0.841 AC: 34960 AN: 41552

American (AMR) AF: 0.656 AC: 10041 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.704 AC: 2440 AN: 3466

East Asian (EAS) AF: 0.731 AC: 3773 AN: 5162

South Asian (SAS) AF: 0.636 AC: 3070 AN: 4830

European-Finnish (FIN) AF: 0.507 AC: 5370 AN: 10592

Middle Eastern (MID) AF: 0.707 AC: 208 AN: 294

European-Non Finnish (NFE) AF: 0.641 AC: 43545 AN: 67980

Other (OTH) AF: 0.690 AC: 1455 AN: 2110

Alfa AF: 0.656 Hom.: 41865

Bravo AF: 0.713

Asia WGS AF: 0.669 AC: 2327 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.55
CADD	Benign	2.4
DANN	Benign	0.40
PhyloP100		-0.49
PromoterAI		0.019	Neutral

Splicing

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

Other links and lift over

dbSNP: rs238288; hg19: chr20-5591903;