rs504750

Variant names:

• chr5-5513918-T-C
• rs504750

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 0.944 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
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.979 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.945 AC: 39277 AN: 41552

American (AMR) AF: 0.876 AC: 13398 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.992 AC: 3444 AN: 3472

East Asian (EAS) AF: 0.624 AC: 3218 AN: 5158

South Asian (SAS) AF: 0.895 AC: 4316 AN: 4822

European-Finnish (FIN) AF: 0.932 AC: 9894 AN: 10612

Middle Eastern (MID) AF: 0.983 AC: 289 AN: 294

European-Non Finnish (NFE) AF: 0.986 AC: 67065 AN: 68046

Other (OTH) AF: 0.948 AC: 2002 AN: 2112

Alfa AF: 0.968 Hom.: 203536

Bravo AF: 0.940

Asia WGS AF: 0.814 AC: 2832 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	8.5
DANN	Benign	0.67
PhyloP100		0.073

Splicing

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

Other links and lift over

dbSNP: rs504750; hg19: chr5-5514031;