chr1-30691029-G-A

Position:

• chr1-30691029-G-A

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 0.267 in 151,832 control chromosomes in the GnomAD database, including 7,657 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 0.27 (7657 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0930

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.524 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: 0.267 AC: 40456 AN: 151714 Hom.: 7638 Cov.: 30

Gnomad AFR AF: 0.530

Gnomad AMI AF: 0.106

Gnomad AMR AF: 0.252

Gnomad ASJ AF: 0.139

Gnomad EAS AF: 0.339

Gnomad SAS AF: 0.242

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.238

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

GnomAD4 genome AF: 0.267 AC: 40529 AN: 151832 Hom.: 7657 Cov.: 30 AF XY: 0.265 AC XY: 19688 AN XY: 74190

Gnomad4 AFR AF: 0.530

Gnomad4 AMR AF: 0.252

Gnomad4 ASJ AF: 0.139

Gnomad4 EAS AF: 0.340

Gnomad4 SAS AF: 0.242

Gnomad4 FIN AF: 0.124

Gnomad4 NFE AF: 0.138

Gnomad4 OTH AF: 0.241

Alfa AF: 0.170 Hom.: 2996

Bravo AF: 0.290

Asia WGS AF: 0.324 AC: 1124 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.1
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1188445; hg19: chr1-31163876;