1-221701342-G-A

Position:

• chr1-221701342-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 0.608 in 152,314 control chromosomes in the GnomAD database, including 29,757 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 0.61 (29687 hom., cov: 30)
  • Exomes 𝑓: 0.58 (70 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.281

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.828 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: 0.607 AC: 92177 AN: 151762 Hom.: 29643 Cov.: 30

Gnomad AFR AF: 0.836

Gnomad AMI AF: 0.652

Gnomad AMR AF: 0.530

Gnomad ASJ AF: 0.511

Gnomad EAS AF: 0.488

Gnomad SAS AF: 0.427

Gnomad FIN AF: 0.562

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.521

Gnomad OTH AF: 0.573

GnomAD4 exome AF: 0.581 AC: 252 AN: 434 Hom.: 70 AF XY: 0.580 AC XY: 152 AN XY: 262

Gnomad4 FIN exome AF: 0.575

Gnomad4 NFE exome AF: 0.750

Gnomad4 OTH exome AF: 1.00

GnomAD4 genome AF: 0.608 AC: 92279 AN: 151880 Hom.: 29687 Cov.: 30 AF XY: 0.604 AC XY: 44824 AN XY: 74210

Gnomad4 AFR AF: 0.836

Gnomad4 AMR AF: 0.530

Gnomad4 ASJ AF: 0.511

Gnomad4 EAS AF: 0.488

Gnomad4 SAS AF: 0.427

Gnomad4 FIN AF: 0.562

Gnomad4 NFE AF: 0.521

Gnomad4 OTH AF: 0.572

Alfa AF: 0.525 Hom.: 35282

Bravo AF: 0.620

Asia WGS AF: 0.479 AC: 1667 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.4
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: rs908857; hg19: chr1-221874684;