rs869807

Variant names:

• chr1-118871849-C-T
• rs869807

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.0462 in 152,242 control chromosomes in the GnomAD database, including 342 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 0.046 (342 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.550
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.39).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.269 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: 0.0463 AC: 7036 AN: 152124 Hom.: 343 Cov.: 32

Gnomad AFR AF: 0.0340

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0246

Gnomad ASJ AF: 0.0144

Gnomad EAS AF: 0.280

Gnomad SAS AF: 0.0868

Gnomad FIN AF: 0.0869

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0340

Gnomad OTH AF: 0.0402

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

GnomAD4 genome AF: 0.0462 AC: 7034 AN: 152242 Hom.: 342 Cov.: 32 AF XY: 0.0493 AC XY: 3671 AN XY: 74414

African (AFR) AF: 0.0340 AC: 1413 AN: 41566

American (AMR) AF: 0.0246 AC: 376 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0144 AC: 50 AN: 3466

East Asian (EAS) AF: 0.281 AC: 1447 AN: 5154

South Asian (SAS) AF: 0.0859 AC: 415 AN: 4832

European-Finnish (FIN) AF: 0.0869 AC: 920 AN: 10582

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.0340 AC: 2315 AN: 68026

Other (OTH) AF: 0.0407 AC: 86 AN: 2112

Alfa AF: 0.0340 Hom.: 48

Bravo AF: 0.0409

Asia WGS AF: 0.155 AC: 542 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.39
CADD	Benign	16
DANN	Benign	0.73
PhyloP100		0.55

Splicing

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

Other links and lift over

dbSNP: rs869807; hg19: chr1-119414472;