1-30052867-A-G

Variant names:

• chr1-30052867-A-G
• rs2860031

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 0.367 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.266 AC: 11011 AN: 41462

American (AMR) AF: 0.394 AC: 6017 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.410 AC: 1424 AN: 3472

East Asian (EAS) AF: 0.457 AC: 2365 AN: 5172

South Asian (SAS) AF: 0.267 AC: 1285 AN: 4818

European-Finnish (FIN) AF: 0.369 AC: 3901 AN: 10576

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.421 AC: 28648 AN: 67974

Other (OTH) AF: 0.371 AC: 784 AN: 2114

Alfa AF: 0.249 Hom.: 595

Bravo AF: 0.368

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.9
DANN	Benign	0.18
PhyloP100		-0.88

Splicing

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

Other links and lift over

dbSNP: rs2860031; hg19: chr1-30525714;