5-54965761-T-C

Variant names:

• chr5-54965761-T-C
• rs1363864

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 0.562 in 152,002 control chromosomes in the GnomAD database, including 25,087 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 0.56 (25087 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.17
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.731 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: 0.562 AC: 85317 AN: 151886 Hom.: 25049 Cov.: 32

Gnomad AFR AF: 0.738

Gnomad AMI AF: 0.477

Gnomad AMR AF: 0.506

Gnomad ASJ AF: 0.519

Gnomad EAS AF: 0.315

Gnomad SAS AF: 0.526

Gnomad FIN AF: 0.523

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.500

Gnomad OTH AF: 0.524

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

GnomAD4 genome AF: 0.562 AC: 85398 AN: 152002 Hom.: 25087 Cov.: 32 AF XY: 0.561 AC XY: 41653 AN XY: 74286

African (AFR) AF: 0.738 AC: 30603 AN: 41470

American (AMR) AF: 0.505 AC: 7702 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.519 AC: 1799 AN: 3468

East Asian (EAS) AF: 0.314 AC: 1626 AN: 5172

South Asian (SAS) AF: 0.526 AC: 2532 AN: 4814

European-Finnish (FIN) AF: 0.523 AC: 5516 AN: 10542

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

European-Non Finnish (NFE) AF: 0.500 AC: 33963 AN: 67958

Other (OTH) AF: 0.519 AC: 1096 AN: 2110

Alfa AF: 0.518 Hom.: 64512

Bravo AF: 0.564

Asia WGS AF: 0.443 AC: 1539 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.19
DANN	Benign	0.49
PhyloP100		-3.2

Splicing

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

Other links and lift over

dbSNP: rs1363864; hg19: chr5-54261589;