rs564041

Variant names:

• chr4-20250644-G-A
• rs564041

Your query was ambiguous. Multiple possible variants found:

• chr4-20250644-G-A
• chr4-20250644-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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;