rs1154435

Variant names:

• chr4-99363991-G-A
• rs1154435

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 0.314 in 151,904 control chromosomes in the GnomAD database, including 8,905 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 0.31 (8905 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252

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 (NFE) allele frequency at 95% confidence interval = 0.409 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: 0.314 AC: 47692 AN: 151786 Hom.: 8898 Cov.: 32

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.227

Gnomad AMR AF: 0.294

Gnomad ASJ AF: 0.286

Gnomad EAS AF: 0.0823

Gnomad SAS AF: 0.307

Gnomad FIN AF: 0.514

Gnomad MID AF: 0.252

Gnomad NFE AF: 0.413

Gnomad OTH AF: 0.285

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

GnomAD4 genome AF: 0.314 AC: 47715 AN: 151904 Hom.: 8905 Cov.: 32 AF XY: 0.315 AC XY: 23386 AN XY: 74272

Gnomad4 AFR AF: 0.145

Gnomad4 AMR AF: 0.294

Gnomad4 ASJ AF: 0.286

Gnomad4 EAS AF: 0.0819

Gnomad4 SAS AF: 0.309

Gnomad4 FIN AF: 0.514

Gnomad4 NFE AF: 0.413

Gnomad4 OTH AF: 0.288

Alfa AF: 0.372 Hom.: 1575

Bravo AF: 0.288

Asia WGS AF: 0.221 AC: 768 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	5.4
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1154435; hg19: chr4-100285148;