rs1035093

chr4-27910121-T-A

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 0.0362 in 152,060 control chromosomes in the GnomAD database, including 218 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 0.036 (218 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0610

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0875 is higher than 0.05.

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: 0.0361 AC: 5485 AN: 151942 Hom.: 216 Cov.: 32

Gnomad AFR AF: 0.0895

Gnomad AMI AF: 0.0318

Gnomad AMR AF: 0.0245

Gnomad ASJ AF: 0.00144

Gnomad EAS AF: 0.0122

Gnomad SAS AF: 0.0416

Gnomad FIN AF: 0.0329

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0103

Gnomad OTH AF: 0.0268

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

GnomAD4 genome AF: 0.0362 AC: 5506 AN: 152060 Hom.: 218 Cov.: 32 AF XY: 0.0373 AC XY: 2771 AN XY: 74342

Gnomad4 AFR AF: 0.0899

Gnomad4 AMR AF: 0.0245

Gnomad4 ASJ AF: 0.00144

Gnomad4 EAS AF: 0.0121

Gnomad4 SAS AF: 0.0411

Gnomad4 FIN AF: 0.0329

Gnomad4 NFE AF: 0.0103

Gnomad4 OTH AF: 0.0265

Alfa AF: 0.0262 Hom.: 13

Bravo AF: 0.0373

Asia WGS AF: 0.0390 AC: 135 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.76
Dann	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1035093; hg19: chr4-27911743;