chr1-202959575-G-A

Position:

• chr1-202959575-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 0.221 in 152,128 control chromosomes in the GnomAD database, including 4,223 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 0.22 (4223 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.530

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.296 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: 0.221 AC: 33630 AN: 152010 Hom.: 4224 Cov.: 32

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.133

Gnomad AMR AF: 0.194

Gnomad ASJ AF: 0.195

Gnomad EAS AF: 0.0470

Gnomad SAS AF: 0.0670

Gnomad FIN AF: 0.234

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.299

Gnomad OTH AF: 0.254

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

GnomAD4 genome AF: 0.221 AC: 33628 AN: 152128 Hom.: 4223 Cov.: 32 AF XY: 0.213 AC XY: 15826 AN XY: 74368

Gnomad4 AFR AF: 0.142

Gnomad4 AMR AF: 0.194

Gnomad4 ASJ AF: 0.195

Gnomad4 EAS AF: 0.0465

Gnomad4 SAS AF: 0.0665

Gnomad4 FIN AF: 0.234

Gnomad4 NFE AF: 0.299

Gnomad4 OTH AF: 0.251

Alfa AF: 0.283 Hom.: 5750

Bravo AF: 0.217

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.18
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6666089; hg19: chr1-202928703;