rs2886117

Variant names:

• chr1-203199753-G-A
• rs2886117

Your query was ambiguous. Multiple possible variants found:

• chr1-203199753-G-A
• chr1-203199753-G-C
• chr1-203199753-G-T

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 0.233 in 152,030 control chromosomes in the GnomAD database, including 5,765 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 0.23 (5765 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00400
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.453 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: 0.233 AC: 35446 AN: 151912 Hom.: 5751 Cov.: 32

Gnomad AFR AF: 0.459

Gnomad AMI AF: 0.158

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.159

Gnomad EAS AF: 0.298

Gnomad SAS AF: 0.143

Gnomad FIN AF: 0.0836

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.215

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

GnomAD4 genome AF: 0.233 AC: 35470 AN: 152030 Hom.: 5765 Cov.: 32 AF XY: 0.231 AC XY: 17161 AN XY: 74324

African (AFR) AF: 0.459 AC: 19000 AN: 41416

American (AMR) AF: 0.223 AC: 3414 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.159 AC: 553 AN: 3468

East Asian (EAS) AF: 0.297 AC: 1531 AN: 5156

South Asian (SAS) AF: 0.143 AC: 689 AN: 4814

European-Finnish (FIN) AF: 0.0836 AC: 885 AN: 10592

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.128 AC: 8730 AN: 67992

Other (OTH) AF: 0.216 AC: 456 AN: 2108

Alfa AF: 0.153 Hom.: 4435

Bravo AF: 0.256

Asia WGS AF: 0.228 AC: 790 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.66
DANN	Benign	0.77
PhyloP100		-0.0040

Splicing

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

Other links and lift over

dbSNP: rs2886117; hg19: chr1-203168881;