1-29712815-A-G

Variant names:

• chr1-29712815-A-G
• rs1866967

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 0.501 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.758

Gnomad4 AMR AF: 0.373

Gnomad4 ASJ AF: 0.483

Gnomad4 EAS AF: 0.395

Gnomad4 SAS AF: 0.417

Gnomad4 FIN AF: 0.432

Gnomad4 NFE AF: 0.402

Gnomad4 OTH AF: 0.468

Alfa AF: 0.416 Hom.: 29513

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1866967; hg19: chr1-30185662;