5-56264200-T-G

Variant names:

• chr5-56264200-T-G
• rs1020388

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 0.34 in 152,088 control chromosomes in the GnomAD database, including 10,932 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 0.34 (10932 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.86
• Publications: 20 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.475 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: 0.340 AC: 51696 AN: 151970 Hom.: 10929 Cov.: 32

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.616

Gnomad AMR AF: 0.364

Gnomad ASJ AF: 0.437

Gnomad EAS AF: 0.0196

Gnomad SAS AF: 0.326

Gnomad FIN AF: 0.432

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.479

Gnomad OTH AF: 0.361

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

GnomAD4 genome AF: 0.340 AC: 51700 AN: 152088 Hom.: 10932 Cov.: 32 AF XY: 0.338 AC XY: 25106 AN XY: 74364

African (AFR) AF: 0.106 AC: 4405 AN: 41544

American (AMR) AF: 0.365 AC: 5567 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.437 AC: 1515 AN: 3466

East Asian (EAS) AF: 0.0199 AC: 103 AN: 5188

South Asian (SAS) AF: 0.328 AC: 1582 AN: 4820

European-Finnish (FIN) AF: 0.432 AC: 4562 AN: 10552

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.479 AC: 32531 AN: 67930

Other (OTH) AF: 0.356 AC: 752 AN: 2114

Alfa AF: 0.426 Hom.: 28231

Bravo AF: 0.327

Asia WGS AF: 0.178 AC: 621 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	15
DANN	Benign	0.84
PhyloP100		1.9

Splicing

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

Other links and lift over

dbSNP: rs1020388; hg19: chr5-55560027;