rs648513

Variant names:

• chr4-17227900-T-C
• rs648513

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 0.586 in 152,010 control chromosomes in the GnomAD database, including 26,410 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 0.59 (26410 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.939
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.602 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.585 AC: 88898 AN: 151892 Hom.: 26368 Cov.: 32

Gnomad AFR AF: 0.598

Gnomad AMI AF: 0.651

Gnomad AMR AF: 0.548

Gnomad ASJ AF: 0.597

Gnomad EAS AF: 0.287

Gnomad SAS AF: 0.559

Gnomad FIN AF: 0.606

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.606

Gnomad OTH AF: 0.568

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

GnomAD4 genome AF: 0.586 AC: 89004 AN: 152010 Hom.: 26410 Cov.: 32 AF XY: 0.583 AC XY: 43324 AN XY: 74296

African (AFR) AF: 0.599 AC: 24812 AN: 41454

American (AMR) AF: 0.548 AC: 8370 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.597 AC: 2069 AN: 3468

East Asian (EAS) AF: 0.287 AC: 1485 AN: 5170

South Asian (SAS) AF: 0.560 AC: 2698 AN: 4814

European-Finnish (FIN) AF: 0.606 AC: 6405 AN: 10564

Middle Eastern (MID) AF: 0.575 AC: 169 AN: 294

European-Non Finnish (NFE) AF: 0.606 AC: 41204 AN: 67942

Other (OTH) AF: 0.569 AC: 1201 AN: 2112

Alfa AF: 0.606 Hom.: 3427

Bravo AF: 0.575

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.5
DANN	Benign	0.64
PhyloP100		-0.94

Splicing

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

Other links and lift over

dbSNP: rs648513; hg19: chr4-17229523;