1-244229543-A-G

Variant names:

• chr1-244229543-A-G
• rs879065

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.271 AC: 11266 AN: 41528

American (AMR) AF: 0.360 AC: 5511 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.423 AC: 1467 AN: 3468

East Asian (EAS) AF: 0.141 AC: 731 AN: 5186

South Asian (SAS) AF: 0.331 AC: 1596 AN: 4818

European-Finnish (FIN) AF: 0.351 AC: 3704 AN: 10562

Middle Eastern (MID) AF: 0.332 AC: 97 AN: 292

European-Non Finnish (NFE) AF: 0.421 AC: 28609 AN: 68004

Other (OTH) AF: 0.372 AC: 785 AN: 2112

Alfa AF: 0.400 Hom.: 20547

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
PhyloP100		0.33

Splicing

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

Other links and lift over

dbSNP: rs879065; hg19: chr1-244392845;