rs1886651

Variant names:

• chr1-29380900-G-A
• rs1886651

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 0.428 in 152,006 control chromosomes in the GnomAD database, including 14,917 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 0.43 (14917 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0800
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.518 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: 0.428 AC: 65053 AN: 151886 Hom.: 14919 Cov.: 32

Gnomad AFR AF: 0.279

Gnomad AMI AF: 0.726

Gnomad AMR AF: 0.356

Gnomad ASJ AF: 0.513

Gnomad EAS AF: 0.314

Gnomad SAS AF: 0.407

Gnomad FIN AF: 0.517

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.523

Gnomad OTH AF: 0.437

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

GnomAD4 genome AF: 0.428 AC: 65071 AN: 152006 Hom.: 14917 Cov.: 32 AF XY: 0.424 AC XY: 31509 AN XY: 74278

African (AFR) AF: 0.279 AC: 11575 AN: 41450

American (AMR) AF: 0.356 AC: 5442 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.513 AC: 1779 AN: 3468

East Asian (EAS) AF: 0.314 AC: 1622 AN: 5160

South Asian (SAS) AF: 0.406 AC: 1954 AN: 4818

European-Finnish (FIN) AF: 0.517 AC: 5455 AN: 10554

Middle Eastern (MID) AF: 0.514 AC: 151 AN: 294

European-Non Finnish (NFE) AF: 0.523 AC: 35513 AN: 67964

Other (OTH) AF: 0.437 AC: 922 AN: 2110

Alfa AF: 0.492 Hom.: 80274

Bravo AF: 0.409

Asia WGS AF: 0.370 AC: 1287 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.5
DANN	Benign	0.82
PhyloP100		0.080

Splicing

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

Other links and lift over

dbSNP: rs1886651; hg19: chr1-29707412;