chr1-244229543-A-G

Variant names:

• chr1-244229543-A-G
• rs879065

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 0.356 in 152,186 control chromosomes in the GnomAD database, including 10,064 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 (10064 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.325

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.417 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.356 AC: 54151 AN: 152068 Hom.: 10053 Cov.: 33

Gnomad AFR AF: 0.271

Gnomad AMI AF: 0.468

Gnomad AMR AF: 0.360

Gnomad ASJ AF: 0.423

Gnomad EAS AF: 0.140

Gnomad SAS AF: 0.331

Gnomad FIN AF: 0.351

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.421

Gnomad OTH AF: 0.373

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

GnomAD4 genome AF: 0.356 AC: 54193 AN: 152186 Hom.: 10064 Cov.: 33 AF XY: 0.352 AC XY: 26183 AN XY: 74378

Gnomad4 AFR AF: 0.271

Gnomad4 AMR AF: 0.360

Gnomad4 ASJ AF: 0.423

Gnomad4 EAS AF: 0.141

Gnomad4 SAS AF: 0.331

Gnomad4 FIN AF: 0.351

Gnomad4 NFE AF: 0.421

Gnomad4 OTH AF: 0.372

Alfa AF: 0.406 Hom.: 16598

Bravo AF: 0.349

Asia WGS AF: 0.282 AC: 981 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.7
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs879065; hg19: chr1-244392845;