1-202069817-T-C

Variant names:

• chr1-202069817-T-C
• rs9427727

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 0.694 in 151,968 control chromosomes in the GnomAD database, including 37,260 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 0.69 (37260 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.804 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: 0.694 AC: 105324 AN: 151850 Hom.: 37226 Cov.: 31

Gnomad AFR AF: 0.812

Gnomad AMI AF: 0.414

Gnomad AMR AF: 0.759

Gnomad ASJ AF: 0.713

Gnomad EAS AF: 0.648

Gnomad SAS AF: 0.764

Gnomad FIN AF: 0.558

Gnomad MID AF: 0.778

Gnomad NFE AF: 0.629

Gnomad OTH AF: 0.702

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

GnomAD4 genome AF: 0.694 AC: 105409 AN: 151968 Hom.: 37260 Cov.: 31 AF XY: 0.695 AC XY: 51605 AN XY: 74262

African (AFR) AF: 0.812 AC: 33658 AN: 41470

American (AMR) AF: 0.759 AC: 11564 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.713 AC: 2476 AN: 3472

East Asian (EAS) AF: 0.649 AC: 3347 AN: 5158

South Asian (SAS) AF: 0.763 AC: 3683 AN: 4828

European-Finnish (FIN) AF: 0.558 AC: 5888 AN: 10544

Middle Eastern (MID) AF: 0.772 AC: 227 AN: 294

European-Non Finnish (NFE) AF: 0.629 AC: 42722 AN: 67958

Other (OTH) AF: 0.698 AC: 1469 AN: 2104

Alfa AF: 0.656 Hom.: 138835

Bravo AF: 0.713

Asia WGS AF: 0.722 AC: 2514 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	7.9
DANN	Benign	0.80
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs9427727; hg19: chr1-202038945;