rs4846567

Variant names:

• chr1-219577375-G-T
• rs4846567

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 81 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0748 AC: 3104 AN: 41508

American (AMR) AF: 0.397 AC: 6053 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.236 AC: 816 AN: 3462

East Asian (EAS) AF: 0.260 AC: 1342 AN: 5154

South Asian (SAS) AF: 0.229 AC: 1101 AN: 4812

European-Finnish (FIN) AF: 0.279 AC: 2946 AN: 10558

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.280 AC: 19040 AN: 67944

Other (OTH) AF: 0.268 AC: 563 AN: 2098

Alfa AF: 0.267 Hom.: 16969

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
PhyloP100		-0.031

Splicing

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

Other links and lift over

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