rs1935881

chr1-190097256-T-C

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 0.281 in 152,052 control chromosomes in the GnomAD database, including 6,546 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 0.28 (6546 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.46

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.352 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: 0.281 AC: 42747 AN: 151934 Hom.: 6543 Cov.: 32

Gnomad AFR AF: 0.173

Gnomad AMI AF: 0.477

Gnomad AMR AF: 0.218

Gnomad ASJ AF: 0.335

Gnomad EAS AF: 0.114

Gnomad SAS AF: 0.283

Gnomad FIN AF: 0.366

Gnomad MID AF: 0.293

Gnomad NFE AF: 0.355

Gnomad OTH AF: 0.282

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

GnomAD4 genome AF: 0.281 AC: 42760 AN: 152052 Hom.: 6546 Cov.: 32 AF XY: 0.278 AC XY: 20697 AN XY: 74326

Gnomad4 AFR AF: 0.173

Gnomad4 AMR AF: 0.218

Gnomad4 ASJ AF: 0.335

Gnomad4 EAS AF: 0.114

Gnomad4 SAS AF: 0.284

Gnomad4 FIN AF: 0.366

Gnomad4 NFE AF: 0.355

Gnomad4 OTH AF: 0.279

Alfa AF: 0.335 Hom.: 17626

Bravo AF: 0.264

Asia WGS AF: 0.199 AC: 690 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.089
Dann	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1935881; hg19: chr1-190066386;