5-72405987-C-T

Variant names:

• chr5-72405987-C-T
• rs2338216

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 0.397 in 152,056 control chromosomes in the GnomAD database, including 13,721 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 0.40 (13721 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.209
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.853 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: 0.397 AC: 60365 AN: 151938 Hom.: 13724 Cov.: 32

Gnomad AFR AF: 0.185

Gnomad AMI AF: 0.376

Gnomad AMR AF: 0.445

Gnomad ASJ AF: 0.413

Gnomad EAS AF: 0.876

Gnomad SAS AF: 0.522

Gnomad FIN AF: 0.519

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.450

Gnomad OTH AF: 0.422

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

GnomAD4 genome AF: 0.397 AC: 60367 AN: 152056 Hom.: 13721 Cov.: 32 AF XY: 0.405 AC XY: 30095 AN XY: 74336

African (AFR) AF: 0.184 AC: 7636 AN: 41492

American (AMR) AF: 0.445 AC: 6798 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.413 AC: 1434 AN: 3472

East Asian (EAS) AF: 0.874 AC: 4535 AN: 5186

South Asian (SAS) AF: 0.522 AC: 2512 AN: 4814

European-Finnish (FIN) AF: 0.519 AC: 5471 AN: 10550

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.450 AC: 30613 AN: 67962

Other (OTH) AF: 0.426 AC: 900 AN: 2112

Alfa AF: 0.433 Hom.: 8027

Bravo AF: 0.384

Asia WGS AF: 0.658 AC: 2286 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.2
DANN	Benign	0.77
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs2338216; hg19: chr5-71701814;