rs648513

chr4-17227900-T-C

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 0.586 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	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

Gnomad4 AFR AF: 0.599

Gnomad4 AMR AF: 0.548

Gnomad4 ASJ AF: 0.597

Gnomad4 EAS AF: 0.287

Gnomad4 SAS AF: 0.560

Gnomad4 FIN AF: 0.606

Gnomad4 NFE AF: 0.606

Gnomad4 OTH AF: 0.569

Alfa AF: 0.606 Hom.: 3427

Bravo AF: 0.575

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	2.5
Dann	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs648513; hg19: chr4-17229523;