rs4845211

chr1-190017615-C-Achr1-190017615-C-T

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 0.718 in 151,766 control chromosomes in the GnomAD database, including 40,255 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 0.72 (40255 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0480

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.901 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: 0.718 AC: 108812 AN: 151648 Hom.: 40177 Cov.: 32

Gnomad AFR AF: 0.909

Gnomad AMI AF: 0.745

Gnomad AMR AF: 0.655

Gnomad ASJ AF: 0.661

Gnomad EAS AF: 0.502

Gnomad SAS AF: 0.669

Gnomad FIN AF: 0.711

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.639

Gnomad OTH AF: 0.688

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

GnomAD4 genome AF: 0.718 AC: 108956 AN: 151766 Hom.: 40255 Cov.: 32 AF XY: 0.717 AC XY: 53144 AN XY: 74154

Gnomad4 AFR AF: 0.909

Gnomad4 AMR AF: 0.656

Gnomad4 ASJ AF: 0.661

Gnomad4 EAS AF: 0.502

Gnomad4 SAS AF: 0.669

Gnomad4 FIN AF: 0.711

Gnomad4 NFE AF: 0.639

Gnomad4 OTH AF: 0.693

Alfa AF: 0.583 Hom.: 2377

Bravo AF: 0.720

Asia WGS AF: 0.633 AC: 2199 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.52
Dann	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4845211; hg19: chr1-189986745;