1-29712815-A-G

Variant names:

• chr1-29712815-A-G
• rs1866967

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 0.501 in 151,848 control chromosomes in the GnomAD database, including 21,032 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 0.50 (21032 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.221
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.751 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: 0.501 AC: 76018 AN: 151730 Hom.: 20991 Cov.: 31

Gnomad AFR AF: 0.758

Gnomad AMI AF: 0.351

Gnomad AMR AF: 0.374

Gnomad ASJ AF: 0.483

Gnomad EAS AF: 0.396

Gnomad SAS AF: 0.417

Gnomad FIN AF: 0.432

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.402

Gnomad OTH AF: 0.469

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

GnomAD4 genome AF: 0.501 AC: 76108 AN: 151848 Hom.: 21032 Cov.: 31 AF XY: 0.501 AC XY: 37182 AN XY: 74204

African (AFR) AF: 0.758 AC: 31415 AN: 41420

American (AMR) AF: 0.373 AC: 5691 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.483 AC: 1674 AN: 3468

East Asian (EAS) AF: 0.395 AC: 2034 AN: 5146

South Asian (SAS) AF: 0.417 AC: 2005 AN: 4810

European-Finnish (FIN) AF: 0.432 AC: 4546 AN: 10524

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.402 AC: 27310 AN: 67918

Other (OTH) AF: 0.468 AC: 986 AN: 2108

Alfa AF: 0.433 Hom.: 53241

Bravo AF: 0.507

Asia WGS AF: 0.387 AC: 1347 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.5
DANN	Benign	0.47
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs1866967; hg19: chr1-30185662;