rs1866967

chr1-29712815-A-Gchr1-29712815-A-T

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;