rs4612655

Variant names:

• chr1-200512699-A-G
• rs4612655

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 0.043 in 152,324 control chromosomes in the GnomAD database, including 200 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 0.043 (200 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0840
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.1 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: 0.0430 AC: 6544 AN: 152206 Hom.: 200 Cov.: 33

Gnomad AFR AF: 0.0118

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.0246

Gnomad ASJ AF: 0.0899

Gnomad EAS AF: 0.00115

Gnomad SAS AF: 0.107

Gnomad FIN AF: 0.0558

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0609

Gnomad OTH AF: 0.0396

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

GnomAD4 genome AF: 0.0430 AC: 6546 AN: 152324 Hom.: 200 Cov.: 33 AF XY: 0.0438 AC XY: 3266 AN XY: 74490

African (AFR) AF: 0.0118 AC: 490 AN: 41586

American (AMR) AF: 0.0246 AC: 376 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0899 AC: 312 AN: 3472

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5194

South Asian (SAS) AF: 0.108 AC: 520 AN: 4822

European-Finnish (FIN) AF: 0.0558 AC: 592 AN: 10616

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0609 AC: 4143 AN: 68016

Other (OTH) AF: 0.0392 AC: 83 AN: 2116

Alfa AF: 0.0407 Hom.: 75

Bravo AF: 0.0370

Asia WGS AF: 0.0390 AC: 135 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	6.9
DANN	Benign	0.85
PhyloP100		0.084

Splicing

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

Other links and lift over

dbSNP: rs4612655; hg19: chr1-200481827;