5-1447745-C-T

Variant names:

• chr5-1447745-C-T
• rs2652510

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 0.458 in 152,012 control chromosomes in the GnomAD database, including 17,988 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 0.46 (17988 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.587 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: 0.458 AC: 69567 AN: 151896 Hom.: 17977 Cov.: 33

Gnomad AFR AF: 0.230

Gnomad AMI AF: 0.603

Gnomad AMR AF: 0.462

Gnomad ASJ AF: 0.592

Gnomad EAS AF: 0.163

Gnomad SAS AF: 0.474

Gnomad FIN AF: 0.558

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.591

Gnomad OTH AF: 0.490

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

GnomAD4 genome AF: 0.458 AC: 69608 AN: 152012 Hom.: 17988 Cov.: 33 AF XY: 0.457 AC XY: 33977 AN XY: 74314

African (AFR) AF: 0.230 AC: 9550 AN: 41502

American (AMR) AF: 0.462 AC: 7056 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.592 AC: 2056 AN: 3472

East Asian (EAS) AF: 0.164 AC: 847 AN: 5168

South Asian (SAS) AF: 0.476 AC: 2292 AN: 4818

European-Finnish (FIN) AF: 0.558 AC: 5879 AN: 10534

Middle Eastern (MID) AF: 0.565 AC: 166 AN: 294

European-Non Finnish (NFE) AF: 0.591 AC: 40173 AN: 67934

Other (OTH) AF: 0.493 AC: 1040 AN: 2110

Alfa AF: 0.558 Hom.: 10412

Bravo AF: 0.437

Asia WGS AF: 0.335 AC: 1168 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.79
DANN	Benign	0.44
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs2652510; hg19: chr5-1447860;