rs504750

Variant names:

• chr5-5513918-T-C
• rs504750

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.944 in 152,280 control chromosomes in the GnomAD database, including 68,311 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 0.94 (68311 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0730

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.979 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: 0.944 AC: 143701 AN: 152162 Hom.: 68256 Cov.: 32

Gnomad AFR AF: 0.945

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.876

Gnomad ASJ AF: 0.992

Gnomad EAS AF: 0.624

Gnomad SAS AF: 0.895

Gnomad FIN AF: 0.932

Gnomad MID AF: 0.984

Gnomad NFE AF: 0.986

Gnomad OTH AF: 0.947

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

GnomAD4 genome AF: 0.944 AC: 143815 AN: 152280 Hom.: 68311 Cov.: 32 AF XY: 0.939 AC XY: 69905 AN XY: 74450

Gnomad4 AFR AF: 0.945

Gnomad4 AMR AF: 0.876

Gnomad4 ASJ AF: 0.992

Gnomad4 EAS AF: 0.624

Gnomad4 SAS AF: 0.895

Gnomad4 FIN AF: 0.932

Gnomad4 NFE AF: 0.986

Gnomad4 OTH AF: 0.948

Alfa AF: 0.973 Hom.: 118497

Bravo AF: 0.940

Asia WGS AF: 0.814 AC: 2832 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	8.5
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs504750; hg19: chr5-5514031;