rs564041

chr4-20250644-G-Achr4-20250644-G-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 0.635 in 152,028 control chromosomes in the GnomAD database, including 31,918 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 0.64 (31918 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00500

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.789 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: 0.636 AC: 96561 AN: 151910 Hom.: 31920 Cov.: 32

Gnomad AFR AF: 0.429

Gnomad AMI AF: 0.830

Gnomad AMR AF: 0.717

Gnomad ASJ AF: 0.775

Gnomad EAS AF: 0.810

Gnomad SAS AF: 0.694

Gnomad FIN AF: 0.681

Gnomad MID AF: 0.706

Gnomad NFE AF: 0.708

Gnomad OTH AF: 0.654

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

GnomAD4 genome AF: 0.635 AC: 96582 AN: 152028 Hom.: 31918 Cov.: 32 AF XY: 0.639 AC XY: 47506 AN XY: 74304

Gnomad4 AFR AF: 0.428

Gnomad4 AMR AF: 0.717

Gnomad4 ASJ AF: 0.775

Gnomad4 EAS AF: 0.809

Gnomad4 SAS AF: 0.693

Gnomad4 FIN AF: 0.681

Gnomad4 NFE AF: 0.708

Gnomad4 OTH AF: 0.655

Alfa AF: 0.691 Hom.: 16873

Bravo AF: 0.632

Asia WGS AF: 0.697 AC: 2423 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	4.0
Dann	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs564041; hg19: chr4-20252267;