1-217425988-G-C

Position:

• chr1-217425988-G-C

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 0.305 in 152,148 control chromosomes in the GnomAD database, including 7,327 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 0.30 (7327 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.580

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.351 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.305 AC: 46332 AN: 152030 Hom.: 7325 Cov.: 33

Gnomad AFR AF: 0.355

Gnomad AMI AF: 0.203

Gnomad AMR AF: 0.243

Gnomad ASJ AF: 0.331

Gnomad EAS AF: 0.0909

Gnomad SAS AF: 0.298

Gnomad FIN AF: 0.221

Gnomad MID AF: 0.439

Gnomad NFE AF: 0.316

Gnomad OTH AF: 0.338

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

GnomAD4 genome AF: 0.305 AC: 46347 AN: 152148 Hom.: 7327 Cov.: 33 AF XY: 0.299 AC XY: 22261 AN XY: 74374

Gnomad4 AFR AF: 0.355

Gnomad4 AMR AF: 0.242

Gnomad4 ASJ AF: 0.331

Gnomad4 EAS AF: 0.0909

Gnomad4 SAS AF: 0.297

Gnomad4 FIN AF: 0.221

Gnomad4 NFE AF: 0.316

Gnomad4 OTH AF: 0.334

Alfa AF: 0.169 Hom.: 334

Bravo AF: 0.305

Asia WGS AF: 0.209 AC: 729 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.018
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12128013; hg19: chr1-217599330;