rs4648889

Variant names:

• chr1-24967338-G-A
• rs4648889

Your query was ambiguous. Multiple possible variants found:

• chr1-24967338-G-A
• chr1-24967338-G-C
• chr1-24967338-G-T

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 0.475 in 151,918 control chromosomes in the GnomAD database, including 18,538 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 0.48 (18538 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.763

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.56).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.688 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: 0.475 AC: 72172 AN: 151800 Hom.: 18510 Cov.: 31

Gnomad AFR AF: 0.287

Gnomad AMI AF: 0.693

Gnomad AMR AF: 0.640

Gnomad ASJ AF: 0.509

Gnomad EAS AF: 0.708

Gnomad SAS AF: 0.670

Gnomad FIN AF: 0.575

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.500

Gnomad OTH AF: 0.509

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

GnomAD4 genome AF: 0.475 AC: 72219 AN: 151918 Hom.: 18538 Cov.: 31 AF XY: 0.491 AC XY: 36419 AN XY: 74236

Gnomad4 AFR AF: 0.287

Gnomad4 AMR AF: 0.640

Gnomad4 ASJ AF: 0.509

Gnomad4 EAS AF: 0.707

Gnomad4 SAS AF: 0.670

Gnomad4 FIN AF: 0.575

Gnomad4 NFE AF: 0.500

Gnomad4 OTH AF: 0.515

Alfa AF: 0.338 Hom.: 899

Bravo AF: 0.473

Asia WGS AF: 0.692 AC: 2405 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
CADD	Benign	18
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4648889; hg19: chr1-25293829;