chr1-163063986-C-G

Variant names:

• chr1-163063986-C-G
• rs28757216

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 0.0719 in 152,174 control chromosomes in the GnomAD database, including 485 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 0.072 (485 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -6.34
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0944 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: 0.0720 AC: 10942 AN: 152056 Hom.: 487 Cov.: 32

Gnomad AFR AF: 0.0165

Gnomad AMI AF: 0.149

Gnomad AMR AF: 0.0918

Gnomad ASJ AF: 0.0893

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.0781

Gnomad FIN AF: 0.122

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0963

Gnomad OTH AF: 0.0799

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

GnomAD4 genome AF: 0.0719 AC: 10938 AN: 152174 Hom.: 485 Cov.: 32 AF XY: 0.0725 AC XY: 5391 AN XY: 74374

African (AFR) AF: 0.0165 AC: 685 AN: 41540

American (AMR) AF: 0.0919 AC: 1403 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0893 AC: 310 AN: 3470

East Asian (EAS) AF: 0.00155 AC: 8 AN: 5176

South Asian (SAS) AF: 0.0779 AC: 376 AN: 4826

European-Finnish (FIN) AF: 0.122 AC: 1294 AN: 10578

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0963 AC: 6550 AN: 67994

Other (OTH) AF: 0.0781 AC: 165 AN: 2112

Alfa AF: 0.0464 Hom.: 39

Bravo AF: 0.0675

Asia WGS AF: 0.0330 AC: 117 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.046
DANN	Benign	0.58
PhyloP100		-6.3

Splicing

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

Other links and lift over

dbSNP: rs28757216; hg19: chr1-163033776;