1-30052867-A-G

Position:

• chr1-30052867-A-G

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 0.367 in 152,054 control chromosomes in the GnomAD database, including 10,598 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 0.37 (10598 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.875

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.442 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: 0.368 AC: 55844 AN: 151936 Hom.: 10603 Cov.: 33

Gnomad AFR AF: 0.266

Gnomad AMI AF: 0.340

Gnomad AMR AF: 0.395

Gnomad ASJ AF: 0.410

Gnomad EAS AF: 0.457

Gnomad SAS AF: 0.266

Gnomad FIN AF: 0.369

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.422

Gnomad OTH AF: 0.375

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

GnomAD4 genome AF: 0.367 AC: 55856 AN: 152054 Hom.: 10598 Cov.: 33 AF XY: 0.366 AC XY: 27205 AN XY: 74342

Gnomad4 AFR AF: 0.266

Gnomad4 AMR AF: 0.394

Gnomad4 ASJ AF: 0.410

Gnomad4 EAS AF: 0.457

Gnomad4 SAS AF: 0.267

Gnomad4 FIN AF: 0.369

Gnomad4 NFE AF: 0.421

Gnomad4 OTH AF: 0.371

Alfa AF: 0.249 Hom.: 595

Bravo AF: 0.368

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.9
DANN	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2860031; hg19: chr1-30525714;