rs1135534

chr4-54228348-C-Achr4-54228348-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.035 in 152,270 control chromosomes in the GnomAD database, including 144 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 0.035 (144 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.57

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.035 (5334/152270) while in subpopulation NFE AF= 0.0415 (2823/68024). AF 95% confidence interval is 0.0402. There are 144 homozygotes in gnomad4. There are 2762 alleles in male gnomad4 subpopulation. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 144 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0351 AC: 5335 AN: 152152 Hom.: 144 Cov.: 32

Gnomad AFR AF: 0.00671

Gnomad AMI AF: 0.175

Gnomad AMR AF: 0.0396

Gnomad ASJ AF: 0.120

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0118

Gnomad FIN AF: 0.0835

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0415

Gnomad OTH AF: 0.0425

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

GnomAD4 genome AF: 0.0350 AC: 5334 AN: 152270 Hom.: 144 Cov.: 32 AF XY: 0.0371 AC XY: 2762 AN XY: 74458

Gnomad4 AFR AF: 0.00669

Gnomad4 AMR AF: 0.0395

Gnomad4 ASJ AF: 0.120

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0120

Gnomad4 FIN AF: 0.0835

Gnomad4 NFE AF: 0.0415

Gnomad4 OTH AF: 0.0416

Alfa AF: 0.0239 Hom.: 15

Bravo AF: 0.0316

Asia WGS AF: 0.00433 AC: 15 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
Cadd	Benign	5.3
Dann	Benign	0.80

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs1135534; hg19: chr4-55094515;