1-214891045-G-A

Position:

• chr1-214891045-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 0.0801 in 152,168 control chromosomes in the GnomAD database, including 651 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 0.080 (651 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.360

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.218 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: 0.0802 AC: 12190 AN: 152052 Hom.: 652 Cov.: 32

Gnomad AFR AF: 0.113

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.0688

Gnomad ASJ AF: 0.0435

Gnomad EAS AF: 0.229

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.0446

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0522

Gnomad OTH AF: 0.0972

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

GnomAD4 genome AF: 0.0801 AC: 12191 AN: 152168 Hom.: 651 Cov.: 32 AF XY: 0.0821 AC XY: 6106 AN XY: 74392

Gnomad4 AFR AF: 0.113

Gnomad4 AMR AF: 0.0686

Gnomad4 ASJ AF: 0.0435

Gnomad4 EAS AF: 0.229

Gnomad4 SAS AF: 0.182

Gnomad4 FIN AF: 0.0446

Gnomad4 NFE AF: 0.0522

Gnomad4 OTH AF: 0.0957

Alfa AF: 0.0612 Hom.: 745

Bravo AF: 0.0819

Asia WGS AF: 0.162 AC: 563 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.45
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11807086; hg19: chr1-215064388;