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. The variant received -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
• Publications: 24 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.287 AC: 11875 AN: 41438

American (AMR) AF: 0.640 AC: 9780 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.509 AC: 1764 AN: 3466

East Asian (EAS) AF: 0.707 AC: 3659 AN: 5172

South Asian (SAS) AF: 0.670 AC: 3221 AN: 4804

European-Finnish (FIN) AF: 0.575 AC: 6057 AN: 10536

Middle Eastern (MID) AF: 0.537 AC: 158 AN: 294

European-Non Finnish (NFE) AF: 0.500 AC: 33994 AN: 67928

Other (OTH) AF: 0.515 AC: 1082 AN: 2102

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
CADD	Benign	18
DANN	Benign	0.86
PhyloP100		0.76

Splicing

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

Other links and lift over

dbSNP: rs4648889; hg19: chr1-25293829;