5-21127549-G-T

Variant names:

• chr5-21127549-G-T
• rs248186

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 0.445 in 151,714 control chromosomes in the GnomAD database, including 18,080 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 0.44 (18080 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.240
• Publications: 1 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 = 0.603 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: 0.445 AC: 67492 AN: 151598 Hom.: 18082 Cov.: 32

Gnomad AFR AF: 0.146

Gnomad AMI AF: 0.431

Gnomad AMR AF: 0.460

Gnomad ASJ AF: 0.635

Gnomad EAS AF: 0.187

Gnomad SAS AF: 0.503

Gnomad FIN AF: 0.583

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.608

Gnomad OTH AF: 0.453

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

GnomAD4 genome AF: 0.445 AC: 67487 AN: 151714 Hom.: 18080 Cov.: 32 AF XY: 0.443 AC XY: 32790 AN XY: 74096

African (AFR) AF: 0.146 AC: 6046 AN: 41400

American (AMR) AF: 0.459 AC: 7004 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.635 AC: 2203 AN: 3472

East Asian (EAS) AF: 0.187 AC: 966 AN: 5154

South Asian (SAS) AF: 0.505 AC: 2434 AN: 4816

European-Finnish (FIN) AF: 0.583 AC: 6129 AN: 10508

Middle Eastern (MID) AF: 0.592 AC: 174 AN: 294

European-Non Finnish (NFE) AF: 0.608 AC: 41189 AN: 67794

Other (OTH) AF: 0.449 AC: 949 AN: 2112

Alfa AF: 0.540 Hom.: 5271

Bravo AF: 0.421

Asia WGS AF: 0.303 AC: 1039 AN: 3430

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.0
DANN	Benign	0.40
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs248186; hg19: chr5-21127658;