rs1504858

Positions:

• chr4-135784795-A-C
• chr4-135784795-A-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 0.819 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.702

Gnomad4 AMR AF: 0.885

Gnomad4 ASJ AF: 0.796

Gnomad4 EAS AF: 0.501

Gnomad4 SAS AF: 0.678

Gnomad4 FIN AF: 0.861

Gnomad4 NFE AF: 0.902

Gnomad4 OTH AF: 0.832

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1504858; hg19: chr4-136705950;