1-221649561-A-G

Position:

• chr1-221649561-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 0.358 in 152,016 control chromosomes in the GnomAD database, including 9,929 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 0.36 (9929 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.71

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.408 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: 0.358 AC: 54347 AN: 151898 Hom.: 9922 Cov.: 33

Gnomad AFR AF: 0.413

Gnomad AMI AF: 0.215

Gnomad AMR AF: 0.353

Gnomad ASJ AF: 0.340

Gnomad EAS AF: 0.280

Gnomad SAS AF: 0.288

Gnomad FIN AF: 0.285

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.349

Gnomad OTH AF: 0.386

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

GnomAD4 genome AF: 0.358 AC: 54394 AN: 152016 Hom.: 9929 Cov.: 33 AF XY: 0.353 AC XY: 26238 AN XY: 74336

Gnomad4 AFR AF: 0.413

Gnomad4 AMR AF: 0.353

Gnomad4 ASJ AF: 0.340

Gnomad4 EAS AF: 0.281

Gnomad4 SAS AF: 0.287

Gnomad4 FIN AF: 0.285

Gnomad4 NFE AF: 0.349

Gnomad4 OTH AF: 0.388

Alfa AF: 0.356 Hom.: 2978

Bravo AF: 0.368

Asia WGS AF: 0.324 AC: 1124 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	9.2
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10495174; hg19: chr1-221822903; COSMIC: COSV60032339;