rs4076635

chr1-5170686-G-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 0.388 in 152,066 control chromosomes in the GnomAD database, including 11,652 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 0.39 (11652 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.339

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.412 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: 0.388 AC: 58972 AN: 151948 Hom.: 11647 Cov.: 32

Gnomad AFR AF: 0.351

Gnomad AMI AF: 0.382

Gnomad AMR AF: 0.363

Gnomad ASJ AF: 0.530

Gnomad EAS AF: 0.275

Gnomad SAS AF: 0.315

Gnomad FIN AF: 0.422

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.417

Gnomad OTH AF: 0.413

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

GnomAD4 genome AF: 0.388 AC: 59003 AN: 152066 Hom.: 11652 Cov.: 32 AF XY: 0.386 AC XY: 28702 AN XY: 74342

Gnomad4 AFR AF: 0.351

Gnomad4 AMR AF: 0.363

Gnomad4 ASJ AF: 0.530

Gnomad4 EAS AF: 0.275

Gnomad4 SAS AF: 0.315

Gnomad4 FIN AF: 0.422

Gnomad4 NFE AF: 0.417

Gnomad4 OTH AF: 0.412

Alfa AF: 0.402 Hom.: 2558

Bravo AF: 0.384

Asia WGS AF: 0.296 AC: 1032 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	1.6
Dann	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4076635; hg19: chr1-5230746;