1-217264584-A-G

Position:

• chr1-217264584-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 0.0321 in 152,168 control chromosomes in the GnomAD database, including 105 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 0.032 (105 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.352

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0689 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: 0.0321 AC: 4881 AN: 152050 Hom.: 105 Cov.: 31

Gnomad AFR AF: 0.0429

Gnomad AMI AF: 0.0636

Gnomad AMR AF: 0.0227

Gnomad ASJ AF: 0.0392

Gnomad EAS AF: 0.000771

Gnomad SAS AF: 0.0742

Gnomad FIN AF: 0.0155

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0288

Gnomad OTH AF: 0.0340

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

GnomAD4 genome AF: 0.0321 AC: 4886 AN: 152168 Hom.: 105 Cov.: 31 AF XY: 0.0327 AC XY: 2437 AN XY: 74414

Gnomad4 AFR AF: 0.0429

Gnomad4 AMR AF: 0.0227

Gnomad4 ASJ AF: 0.0392

Gnomad4 EAS AF: 0.000773

Gnomad4 SAS AF: 0.0753

Gnomad4 FIN AF: 0.0155

Gnomad4 NFE AF: 0.0288

Gnomad4 OTH AF: 0.0336

Alfa AF: 0.0335 Hom.: 8

Bravo AF: 0.0325

Asia WGS AF: 0.0210 AC: 74 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.2
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10495052; hg19: chr1-217437926;