rs1504858

Variant names:

• chr4-135784795-A-C
• rs1504858

Your query was ambiguous. Multiple possible variants found:

• chr4-135784795-A-C
• chr4-135784795-A-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 0.819 in 151,426 control chromosomes in the GnomAD database, including 51,637 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 0.82 (51637 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.44
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.896 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: 0.819 AC: 123847 AN: 151304 Hom.: 51592 Cov.: 30

Gnomad AFR AF: 0.702

Gnomad AMI AF: 0.831

Gnomad AMR AF: 0.885

Gnomad ASJ AF: 0.796

Gnomad EAS AF: 0.502

Gnomad SAS AF: 0.677

Gnomad FIN AF: 0.861

Gnomad MID AF: 0.825

Gnomad NFE AF: 0.902

Gnomad OTH AF: 0.838

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

GnomAD4 genome AF: 0.819 AC: 123943 AN: 151426 Hom.: 51637 Cov.: 30 AF XY: 0.814 AC XY: 60199 AN XY: 73988

African (AFR) AF: 0.702 AC: 29035 AN: 41342

American (AMR) AF: 0.885 AC: 13398 AN: 15144

Ashkenazi Jewish (ASJ) AF: 0.796 AC: 2754 AN: 3458

East Asian (EAS) AF: 0.501 AC: 2562 AN: 5110

South Asian (SAS) AF: 0.678 AC: 3268 AN: 4818

European-Finnish (FIN) AF: 0.861 AC: 9101 AN: 10568

Middle Eastern (MID) AF: 0.827 AC: 243 AN: 294

European-Non Finnish (NFE) AF: 0.902 AC: 61079 AN: 67682

Other (OTH) AF: 0.832 AC: 1745 AN: 2098

Alfa AF: 0.851 Hom.: 6927

Bravo AF: 0.818

Asia WGS AF: 0.623 AC: 2168 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.22
DANN	Benign	0.38
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs1504858; hg19: chr4-136705950;