rs4846567

chr1-219577375-G-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 0.231 in 151,984 control chromosomes in the GnomAD database, including 4,933 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 0.23 (4933 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0310

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.5).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.389 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: 0.231 AC: 35085 AN: 151866 Hom.: 4928 Cov.: 31

Gnomad AFR AF: 0.0750

Gnomad AMI AF: 0.0637

Gnomad AMR AF: 0.397

Gnomad ASJ AF: 0.236

Gnomad EAS AF: 0.260

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.279

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.280

Gnomad OTH AF: 0.268

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

GnomAD4 genome AF: 0.231 AC: 35097 AN: 151984 Hom.: 4933 Cov.: 31 AF XY: 0.234 AC XY: 17374 AN XY: 74286

Gnomad4 AFR AF: 0.0748

Gnomad4 AMR AF: 0.397

Gnomad4 ASJ AF: 0.236

Gnomad4 EAS AF: 0.260

Gnomad4 SAS AF: 0.229

Gnomad4 FIN AF: 0.279

Gnomad4 NFE AF: 0.280

Gnomad4 OTH AF: 0.268

Alfa AF: 0.270 Hom.: 7005

Bravo AF: 0.239

Asia WGS AF: 0.244 AC: 846 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.50
Cadd	Benign	0.89
Dann	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4846567; hg19: chr1-219750717; COSMIC: COSV60029493;