rs2250107

Variant names:

• chr5-123960453-G-A
• rs2250107

Your query was ambiguous. Multiple possible variants found:

• chr5-123960453-G-A
• chr5-123960453-G-C
• chr5-123960453-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 0.681 in 152,014 control chromosomes in the GnomAD database, including 36,618 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 0.68 (36618 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.310
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.908 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.681 AC: 103403 AN: 151898 Hom.: 36544 Cov.: 32

Gnomad AFR AF: 0.860

Gnomad AMI AF: 0.629

Gnomad AMR AF: 0.647

Gnomad ASJ AF: 0.514

Gnomad EAS AF: 0.930

Gnomad SAS AF: 0.704

Gnomad FIN AF: 0.677

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.570

Gnomad OTH AF: 0.626

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

GnomAD4 genome AF: 0.681 AC: 103546 AN: 152014 Hom.: 36618 Cov.: 32 AF XY: 0.687 AC XY: 51024 AN XY: 74290

African (AFR) AF: 0.860 AC: 35703 AN: 41492

American (AMR) AF: 0.648 AC: 9888 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.514 AC: 1784 AN: 3468

East Asian (EAS) AF: 0.930 AC: 4821 AN: 5182

South Asian (SAS) AF: 0.706 AC: 3398 AN: 4816

European-Finnish (FIN) AF: 0.677 AC: 7133 AN: 10540

Middle Eastern (MID) AF: 0.555 AC: 162 AN: 292

European-Non Finnish (NFE) AF: 0.570 AC: 38754 AN: 67944

Other (OTH) AF: 0.630 AC: 1331 AN: 2112

Alfa AF: 0.603 Hom.: 14235

Bravo AF: 0.688

Asia WGS AF: 0.838 AC: 2913 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	6.5
DANN	Benign	0.18
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs2250107; hg19: chr5-123296147;